The council’s culture spokesperson, councillor Martin Grieg, said “considerable efforts” had been made to make sure staff knew what was within the collection.
He told BBC Radio Scotland’s Lunchtime Live programme: “There are occasions where artefacts are stored and not properly indexed.
“We have put in place a very robust system of making sure we have up to date reports and records of all the items in the collection.
“There will be a proportion that have been stolen, a proportion will have been misfiled, in the wrong place or mis-labelled, so there is work underway to find out exactly what we have and where.”
Aberdeen City Council said it had published information on the missing items on its emuseum site.
In 2022, the authority said the losses had happened over many years and even decades.
Only about 10% of the items currently recorded as missing have been photographed, and some may have been mislaid during the moving of large sections of the collection.
