Ports slid towards chaos last week as a major electronic customs clearance system tried to migrate from its mainframe to a Windows-based system.
Community Network Services announced today at 13:00 that it had reverted to its mainframe system and that queues were at their normal status.
But last week the gradual degradation of the new system had meant that freight forwarders and customs agents had to revert to manual processing at Southampton and Tilbury.
Containers were stuck at berths waiting for clearance. Courier operations at Heathrow, Stansted and East Midlands airports were also affected.
CNS staff worked over the weekend in a race against time to have the mainframe and its network up and running and to clear backlogs.
The company handles about 35 per cent of the UK's imports and exports over a nationwide network and is a subsidiary of Southampton Container Terminals.
Freight forwarder association Bifa is reported to be pressing for compensation.