The LTTE is fighting for independence for the island's minority 2.
5 million Tamil community. The conflict has claimed more than 60,000 lives since 1972.
The civilians crossed over to government-held areas on Sunday, the ministry said. Residents have been fleeing the Vakarai area, held by the Liberation Tigers of Tamil Eelam (LTTE), following heavy exchanges of artillery and mortar bomb attacks in recent weeks.
The defence ministry said a total of 16,139 people had crossed over to government-held areas since the beginning of November.
"The security forces have accommodated them and provided them with food, medicine and other facilities," the ministry said in a statement.
Sri Lanka's army chief Sarath Fonseka said last week that troops will move to clear the eastern province of Tamil Tiger rebels.
The United Nations and international truce monitors have voiced grave concern for 35,000 "desperate civilians" caught in the crossfire between Sri Lankan troops and Tamil rebels.
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The Norwegi