Amnesty said it had received reports that the government is housing those who have been able to leave LTTE areas in temporary shelters that often operate as de facto detention centres.
"Both sides to this long conflict have again shown that they will jeopardise the lives of thousands of ordinary people in the pursuit of military objectives," Foster said.
"In the absence of independent international monitors, Sri Lankan civilians lack protection and remain at the mercy of two forces with long records of abuse," she added.
Neither side to the conflict commented on Amnesty's statement.
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But Sri Lanka's defence ministry said Friday that 39 Tiger rebels and five soldiers had died in clashes across the island's northern front on Thursday.
The LTTE, who have been fighting for a separate homeland since 1972, did not comment on the ministry statement.
The latest government figures raise the number of rebels reported killed by government troops to 5,859 since Januar