The site was discovered by a group of people who were digging a well on Tuesday.
"We are not sure if it is a mass grave. Several bones were unearthed. It could belong to one person or several people," said police spokesman Ranjith Gunasekara.
The eastern district was the scene of heavy fighting between government troops and Tamil Tigers up to one year ago, when the rebels were ejected from the area.
Gunasekara could not say how long the bones had been there.
"The area judge visited the site today (Wednesday) and we have to wait for his report," he said.
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Elsewhere, the military said troops overran a rebel base in the guerrilla-held northern town of Vidattaltivu on Wednesday.
The defence ministry also said that fighting in the north on Tuesday left 31 rebels and one soldier dead.
The deaths raise the number of rebels killed by troops since January to 4,987, while 442 soldiers have died in combat over the same period, according to defence ministry figures.
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