Several tons of frozen fish ended up costing Rye Partnership more than £40,000.
The incident came to light at the Partnership’s recent AGM at Tilling Green Community Centre.
Partnership member Cllr Sam Souster explained: “The fish quay building is owned by the Environment Agency and sub-let by Rye Partnership, who have it on a very long lease.
“We had problems with a tenant who eventually went out of business and it cost us thousands of pounds to clear up.”
Partnership chairman Keith Glazier faced questions at the meeting as to why the organisation had accounts showing a loss of £96,000 for the year.
He said a new tenant has now been found and the Partnership hoped to develop a regeneration plan for the area in the vicinity of the fishing quay.
Cllr Glazier said the accounts were not considered a major loss and did not give the Partnership any cause for concern.
Cllr Souster said: “Rye Partnership has always acted for the right reasons. They did some good things when the money was available - it isn’t now so the Partnership has to operate in a different way.
“There are some issues such as the website. The Partnership has been promising for years to sort its website out and that has still not happened.
“People say they have problems keeping up to date with Partnership activities. “
Rye Partnership played a key role in the refurbishment of the Women’s Tower in Rye and ran the well received Women and Children of Re project.