Men, women and children, clutching their few belongings in canvas bags, boarded buses to return to Jaffna, Batticaloa, Trincomalee and Ampara.
They had been housed in state-run camps in the northern district of Vavuniya, 260 kilometres (160 miles) north of Colombo.
Wednesday's batch of relocations was the first in the government's efforts to resettle by the end of the year at least 80 percent of the 300,000 displaced people.
Tens of thousands of those who fled the war zone are housed in tightly-guarded camps to which international observers and aid agencies have not been given free access.
The United Nations and western governments have urged Sri Lanka to allow people to return to their homes quickly.
The government said it would allow resettlement once minefields were cleared and the refugees had been screene