"About 5,000 responded to the general amnesty we had from May 2 to the 30th," Brigadier Udaya Nanayakkara said.
"We are now trying to get at 11,000 to 12,000 deserters who did not respond to the amnesty.
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He said most of the desertions had taken place several years ago, and asserted that there had been no exodus in recent years despite heavy fighting with separatist Tamil Tiger guerrillas.
In 2003, the government moved to legally discharge from the security forces some 51,000 deserters if they agreed to pay any money they owed the military, while those wanting to rejoin were considered for fresh enlistment.
However, military officials said despite that offer, thousands were still listed as deserters in the ranks of Sri Lankan security personnel numbering about 200,000.
Sri Lankan security forces are locked in combat with Tamil Tiger rebels whose strength is not known, but estimated at between 5,000 to 15,000.
A 2002 Norwegian-arranged truce began to unravel from Decemb