The RPA suspended 17 out of 39 organisations on the scheme last year, claiming they were in breach of Fresh Fruit & Vegetables Aid Scheme requirements and giving them until last week to submit evidence of having made sufficient changes to be re-admitted.
But evidence was still being submitted right up to the deadline of midnight on 9 August from five unnamed organisations that were in danger of being dropped from the scheme, according to an RPA representative.
"We are listening to representations up to the wire," she said, adding: "We don't have the final say (on re-admittance) - that needs ministerial sign-off."
Earlier, external relations director Sharon Ellis defended the RPA's handling of the affair. "It's not just in the UK. Other member states have seen disallowances," she said. "The 22 compliant organisations have continued to trade successfully and get more than £26m a year.
"That's good for the industry and the economy and we want to protect that. But we had a duty to the taxpayer to ensure we had robust evidence to show the European Commission's auditors."
The RPA will meet the auditors shortly "to convince them there are no further shortcomings", she said, adding: "The commission is consulting until September on how the scheme is run in future, as part of the reform of the common agricultural policy, and we encourage the industry to engage with that."