The Alpine country this week repatriated the final 68 looted artifacts to its southern neighbour, ending a restitution process that began in 2001, the ministry said in a statement.
"This restitution marks the end of a procedure of judicial mutual assistance that has lasted for years and has allowed for the return of a total of 4,536 objects," it said.
Switzerland still has several hundred objects seized from art dealers in its possession, Basel public prosecutor spokesman Peter Gill told AFP.
"We are still trying to determine their origin," he said, adding that they did not come from Italy.
Italian authorities requested Switzerland's help with the case in 2001 after uncovering a criminal gang – including an antiques dealer, businessmen, a banker and others – that had been smuggling artifacts out of the country.
Swiss prosecutors have since seized some 5,800 objects, most of which came from illegal digs in Italy, including around 100 archaeological treasures from the Etruscan and Roman periods.
Five icons were also found to have been stolen in Greece and returned to Greek authorities.