Around 1,000 pairs of shoes are being donated to the detention services.
The shoes, which are not counterfeit, had been impounded because they had been used to conceal other items.
Addressing a news conference at the Customs Department, Finance Minister Edward Scicluna explained that counterfeit items were destroyed because they could not be distributed due to court orders.
There were instances when genuine products were auctioned, such as household appliances, cars and jewellery.