UN Secretary-General Ban Ki-moon said he was deeply troubled by the findings.
The Indian authorities say they are investigating the allegations and the vice chief of the Indian army had visited Congo in May to look into them.
India has said it will take strict action against the perpetrators if the allegations are proved.
One UN official said there may have been abuse of young girls and boys by at least 10 Indian peacekeepers.
A UN statement said an internal investigation "revealed prima facie evidence" that the Indian troops in the UN's Congo mission Monuc "may have engaged in sexual exploitation and abuse".
The cases occurred over a period of several years, a UN official told Agence France-Presse and the troops were now back in India.
The UN statement said Mr Ban "reiterates, in the strongest possible terms, that such behaviour, if substantiated, is wholly unacceptable".
No further details were released of the allegations.
But UN officials say the cases occurred in North Kivu province, where peacekeepers have been policing a truce between the government and militiamen.