In 2003, the government moved to legally discharge from the security forces 51,000 deserters.
Tens of thousands were killed in Sri Lanka's decades-old Tamil separatist conflict. The pardon applied to deserters serving up to a year in jail after being convicted by a military court.
The amnesty announcement coincided with Poson, the celebration of the arrival of Buddhism in Sri Lanka more than 2,500 years ago.
"They were released from the main prison in Colombo and several other jails across the country," an official said.
Most of the desertions took place several years ago, a military official said, adding there had been no exodus in recent years despite heavy fighting with separatist Tamil Tiger guerrillas who were eventually defeated last month.