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Exporters at Heathrow Airport said that at one point they reverted to a largely manual process of sending staff to visit customs officials in person to clear goods for export, instead of exchanging electronic messages to gain authorisation.
Customs has since issued an apology to organisations linked to its Customs Handling of Import and Export of Freight (Chief) system. It said there had been technical problems at a time when the system was processing a record number of customs declarations.
The difficulties mirrored the experiences of other public sector bodies such as Inland Revenue and the Passport Service, which found the quality of their service to customers was hit badly in the weeks following the introduction of a major new system.
Organisations linked to Chief had slow response times after Customs introduced the new export system component for the air freight community in July. The system replaced paper Customs declarations with electronic submissions and led to exporters changing their business processes and in some cases their software.
After going live to the air freight community, the new export system was hit by hundreds of spurious messages sent by malfunctioning software run by a third-party company on behalf of a freight agent. All this happened over a single consignment of goods and prompted Customs to invoke fall-back procedures.
Having solved this problem, Customs found that there were other glitches with Chief which caused slow response times for exporters.
The problems were reported to Syntegra, the supplier of the Chief system, which worked around the clock to devise fixes.
Last week a spokesman for Customs & Excise said the problems have been fixed and now Chief is "working perfectly".