The thieves targeted a collection known as the Treasure of Benghazi.
It included more than 10,000 pieces, with coins dating back to Greek, Roman, Byzantine and early Islamic times, but also other treasures such as small statues and jewellery.
Most had been discovered during the Italian occupation of Libya and were taken out of the country.
They were then returned to Libya in 1961 after the country's independence.
The collection has been kept in the vault of the Commercial Bank of Benghazi ever since, waiting for the opening of a museum that was never built.
The coins were never photographed or documented and seemed to have been forgotten, according to Dr Saleh Algab, the chairman of the Tripoli Museum.
Although not the only collection of ancient coins in Libya, Mr Algab said they were a hugely valuable representation of the mosaic of Libyan history - an important reminder for Libya's sometimes fractious, at times antagonistic, regions and ethnic groups that they all belong in one Libya, he said.
BBC News - Looted Libyan treasure 'in Egypt':