Salvage contractors this week recovered 69 of them from the hull of the rotted display vessel Rowitta, which is being pulled apart for removal.

More are expected to be found when her remains are lifted out of the village harbour mud in the next week.

For Flagstaff Hill manager Peter Abbott and staff it was a welcome relief after enduring more than three months of criticism and conjecture about discrepancies in the number of items in the collection. Critics claimed there were none in the Rowitta.

A total of 872 ingots and 10 copper sheets from the 1878 wreck were loaned to Warrnambool by the Commonwealth in 1984 under a written agreement.

In subsequent years the ingots were moved to various locations around the village. Seven were loaned for ballast in Port Fairy’s historic lifeboat and one to Port Campbell for display at the local museum/information centre, before Mr Abbott’s tenure.

Theories surfaced late last year after a city council meeting agenda mentioned discrepancies in recent audits at Flagstaff Hill — 728 ingots recorded in 2012 and 652 last year.

Mr Abbott maintained there would be a significant number in the two display vessels and predicted the shortfall would be resolved.

On calculations by The Standard yesterday there were still  84 unaccounted for. 

Mr Abbott said the recovery from Rowitta’s hull went some way to disproving the critics.

“We want to get her hull out of the water before doing another full count,” he said.

“And we’ll send a diver in to search around the harbour mud. We’ll also do a re-count in the Reginald M, especially underneath the deck.

“The ingots were loaned for display purposes and ballast, which is exactly what some were used for in our display vessels.”

He said staff and volunteers had been unfairly criticised.

"It was demoralising for them as they were honestly going about their work of recording our collection," Mr Abbott said.

"I've seen commentary alleging staff and volunteers must have been stealing them.

"Our collections volunteers are passionate, hard working and diligent - they've been upset by the allegations.

"Discrepancies are a normal part of museum collection audits."

Mr Abbott said allegations about copper sheets being vandalised were also off target.

One partially-complete sheet had encrustation on its jagged edge indicating it had already been cut when salvaged from the wreckage location near Port Campbell.

Another had a small V-cut after a piece was removed to make a book clasp for display during the Mary Rose exhibition in 1995, Mr Abbott said.

A third had a hole drilled in it to fasten to a wall at Port Campbell which triggered a written apology.

"There has been no deliberate attempt by staff or volunteers to destroy history," he said.