TMS Security Incident Response: The 72-Hour Recovery Protocol That Saved Operations During Critical System Breaches

Your TMS security incident response playbook just became your most valuable asset. Cyber incidents in logistics jumped 61% in 2025, with cybersecurity incidents rising 48% over five years and major cyberattacks surging from 12 incidents in 2020 to 60 projected in 2025. The average data breach in transport costs $4.18 million, while the shipping sector alone suffered 64 state-sponsored attacks in 2024.

Transportation now ranks among the 10 sectors most affected by ransomware, with 223 affected organisations. When attackers hit your TMS, you have a 72-hour window to contain damage, preserve evidence, and restore operations before cascading failures trigger supply chain chaos. This protocol has saved companies millions while their competitors struggled through weeks of downtime.

TMS Security Incidents Are Escalating—Your 72-Hour Window

The numbers paint a stark picture. Transportation and shipping generated the most threat detections in Q4 2024 and the second most in Q1 2025, with detected threats rising 11%. State-sponsored groups from Russia, China, and Iran simultaneously targeted maritime infrastructure, airport systems, and transportation networks across multiple countries.

TMS systems are prime targets for three reasons. As central components of critical infrastructure, transportation and logistics systems serve as high-value attack vectors for threat actors seeking data theft, service disruption, or system compromise, with 70% of 2024 attacks involving critical infrastructure. Second, they hold treasure troves of carrier data, shipment visibility, and financial transactions. Third, successful attacks create ripple effects across entire supply chains.

Transportation companies take 192 days on average to detect a breach and another 60 days to contain it. You can't afford that timeline. When systems like Manhattan Active, Blue Yonder, E2open, Descartes, or Cargoson face security incidents, the clock starts ticking immediately.

Hour 0-6: Immediate Containment and Assessment

Your first six hours determine whether you survive or join the companies that never fully recovered. Had a global shipping company's systems been offline for even a few hours in February 2025, the cascading effect would have impacted trade and industry worldwide. They detected and contained their ransomware attack in 14 minutes.

Activate your incident response team within 15 minutes. Your team needs predefined roles: incident commander, technical lead, communications lead, legal counsel, and external vendor contacts. Isolate affected systems quickly by disconnecting infected warehouse devices. Cut network connections to prevent lateral movement, but document everything first.

Preserve critical evidence before containment actions destroy it. Capture memory dumps from infected systems, network traffic logs, and user session data. Use SIEM tools and anomaly detection for identification, then isolate affected systems quickly.

TMS-Specific Containment Actions

Disable API connections immediately. Your TMS integrations with carriers, 3PLs, and ERP systems become attack highways. Suspend EDI transactions and webhook processes. A ransomware attack on a TMS can completely halt operations, preventing shipments, delaying deliveries, and disrupting the entire supply chain.

Secure your freight billing and financial data flows by isolating payment processing systems. Preserve shipment tracking and delivery confirmations by maintaining read-only access where possible. Document carrier notification requirements immediately—some contracts require breach notification within hours.

Hour 6-24: Investigation and Impact Analysis

Now you investigate while containment holds. Remove malware, revoke compromised credentials, restore systems from clean backups, and identify root cause through post-incident analysis. Conduct forensic analysis to understand the breach extent and malware type, as attack severity affects recovery time.

Assess customer and carrier data exposure systematically. TMS contain sensitive data including customer shipping addresses and contact information, confidential carrier contracts with pricing and service agreements, shipment details about goods and destinations, and financial data with invoice information. Map every compromised data type to regulatory notification requirements.

Your regulatory clock starts ticking. SOC 2 compliance, GDPR requirements, and industry-specific mandates have strict reporting timelines. Compliance typically requires implementing technical controls, continuous monitoring, employee training, incident response planning, and reinforced supply-chain security under regulations like NIS2.

Evidence Collection in Multi-Carrier Environments

Preserve EDI transaction logs that show the attack timeline and affected trading partners. Collect carrier API audit trails and webhook failure logs. Cross-reference with integration points from systems like nShift, Shippo, MercuryGate, and Cargoson to understand lateral movement paths.

Document every system interaction. Attackers frequently use web-facing assets and remote services to gain a foothold, then leverage third-party access to move laterally through systems. Your evidence collection determines whether you can prosecute attackers and recover insurance claims.

Hour 24-48: Recovery Planning and Execution

Recovery prioritization separates successful responses from disasters. Restore systems from clean backups and invoke disaster recovery plans to restore warehouse management systems from immutable backups. Cloud computing services typically include data backups as part of subscriptions, with data backed up incrementally and switchable to different computing environments with full data recovery.

Without an effective disaster recovery plan or backup solutions in place, the recovery process becomes more time-consuming. Test your clean backups before restoration. Schedule frequent backups for real-time shipment tracking data and store backups both on-site and in secure cloud storage.

Deploy restoration on clean bare metal servers or fresh cloud resources. Avoid warm standby sites that might be infected. Run staged environment testing before production restoration to verify system integrity and performance.

TMS-Specific Recovery Priorities

Restore core freight management functions first: rating engines, routing optimization, and tracking systems. These generate immediate revenue and customer satisfaction. Next, recover carrier connectivity and label generation systems—without these, shipments stop completely.

Customer portals and visibility tools come third, followed by ERP and WMS integrations. Computer systems are so intrinsic to transportation operations that businesses cannot run without them—they can't get new loads, take shipper orders, dispatch existing orders, or invoice for anything.

Hour 48-72: Operational Restoration and Hardening

Your final 24 hours focus on validation and hardening. Recovery Time Objectives and Recovery Point Objectives must match operational needs, while logistics redundancy includes backup carriers, alternate ports, and secondary suppliers. Test every restored system under production load before declaring recovery complete.

Implement enhanced authentication during user access restoration. Multi-factor authentication (MFA) and role-based access control (RBAC) ensure only authorized personnel can access sensitive data. Implement rigorous patch management programs to ensure all software, including TMS, stays updated, automating this process where possible.

Deploy post-incident monitoring and alerting. Implementing robust monitoring and detection systems is crucial for identifying and responding to potential security breaches in real-time using intrusion detection and prevention systems, log analysis, and security information and event management (SIEM) solutions.

Major TMS vendors like Manhattan Active, Blue Yonder, E2open, Descartes, and Cargoson have built-in security monitoring, but you need additional layers for comprehensive protection.

Post-Incident: Lessons Learned and Future-Proofing

Document everything while memories remain fresh. Developing and regularly updating incident response plans helps companies respond swiftly and effectively to ransomware attacks, minimizing disruption and damage. Conducting executive tabletop exercises post-incident refines playbooks, with proper preparation enabling five-day recovery that, while painful, remains survivable versus companies that might not have recovered at all.

Learning from broader trends matters. Research shows that only 10% of 2025 ransomware victims recovered more than 90% of their data. Critical elements of effective ransomware recovery plans include incident response preparation, backup solutions, network protection measures, and robust disaster recovery planning.

Having a robust disaster recovery plan ensures quick restoration of logistics management solutions. Treat backup as a fundamental element of broader resilience strategy with data recovery orchestration and regular testing.

Schedule quarterly tabletop exercises and annual live-fire drills. Run tabletop exercises through scenarios like ransomware locking down port terminals, red-team/blue-team drills where attackers simulate breaches while defenders practice responses, and executive war games where leadership rehearses decision-making under time pressure.

TMS Security Incident Response Checklist and Templates

Hour 0-6 Immediate Response:

• Activate incident response team within 15 minutes
• Preserve memory dumps and network traffic logs
• Isolate infected systems while documenting connections
• Disable TMS API connections and EDI transactions
• Secure freight billing and financial data flows

Hour 6-24 Investigation:

• Conduct forensic analysis of breach scope and malware type
• Assess customer and carrier data exposure levels
• Trigger regulatory notification requirements
• Preserve EDI logs and carrier API audit trails
• Document attack vectors through system integrations

Hour 24-48 Recovery:

• Test clean backups before restoration begins
• Deploy on fresh infrastructure avoiding compromised systems
• Restore core freight management functions first
• Recover carrier connectivity and label generation second
• Test staged environments before production deployment

Hour 48-72 Hardening:

• Validate all systems under production load
• Implement enhanced authentication with MFA
• Deploy comprehensive monitoring and alerting
• Apply security patches across all systems
• Document lessons learned for future incidents

When cyber incidents strike your TMS, this 72-hour protocol provides your roadmap to survival. The true measure of resilience isn't avoiding every attack, but detecting, containing, and recovering without catastrophic disruption, as downtime can halt factories, idle ships, and empty store shelves. Save this playbook, customize it for your environment, and pray you never need it. But when that day comes, you'll be ready.