"After months of turmoil and indecision we have clarity on historical invoicing," said FPC chief executive Nigel Jenney. "This affects importers of fruit, vegetables or cut flowers."
Problems stemmed from Government changes to paperwork for inspections of fresh produce from non-EU countries that needed phytosanitary certificates.
A long-running revision of its IT notification system, called PEACH, meant invoices for inspections and identity checks had not been issued since this March.
"Defra has confirmed that companies will not be charged for imports notified to PEACH from 1 March 2008 to 31 October 2008," he said.
New procedures for plant-health imports are to be introduced by the Government from 18 November. From then, the Government will need a quarantine-release certificate after inspection to secure the release of plants into circulation.