A rise in attacks on Iraqi Christians was, in part, blamed on Kurdish groups which feared minority representation could jeopardize recognition of Kurdistan’s population as Kurds.
The bill will give minorities a quota of six out of a total of 440 provincial council seats to be elected by January 31.
Naseer al-Ani, chief of staff for the presidency council, said: "In order to fix the rights of the minority seats in the future, the presidency council decided to approve the decision voted on before by the parliament."
In the days up to Saturday's decision, Christian groups had petitioned Iraqi officials in an attempt to get more seats.
Yunadim Kanna, a Christian member of parliament, told Reuters: "We completely reject this approval. This appeases the ethnic and religious ignorance of the parliament.
"It is a disappointment and depressing to Christians in Iraq. It is deeply regrettable."
The presidency council includes Jalal Talabani, the president, who is a Kurd, and his vice-presidents, a Sunni Arab and a Shia.
In a statement, the presidency council said: "The most important thing that has been achieved in all these talks is the right of minorities through fixed seats."