The ex-gratia was sanctioned from the Prime Minister's National Relief Fund, the PMO said in a statement.
"Prime Minister has expressed his deep anguish over the loss of lives in the recent communal clashes in Muzaffarnagar district of Uttar Pradesh," it added.
Singh condemned the violence on Monday and assured chief minister Akhilesh Yadav of all required help from the Centre in dealing with the situation.
The Prime Minister gave the assurance while speaking to the chief minister about the steps being taken to restore peace in the areas which have witnessed violence.
Muzaffarnagar has been in the grip of violence for last few days and Army has been called in to assist the civil administration.