It was not immediately clear who was behind the assault on Camp Liberty, a former US military base on the western outskirts of the capital housing about 3,000 members of the People's Mujahedeen of Iran, or the Mujahedeen-e-Khalq (MEK).
The United Nations mission in Iraq called for an immediate probe and said monitors were following up on the deaths, while the UN High Commissioner for Refugees condemned what he called a "despicable act of violence."
Five members of the People's Mujahedeen were killed by the mortar rounds and rockets, according to two Iraqi security officials who spoke on condition of anonymity.
The attack also wounded at least 40 members of the group and three Iraqi policemen, they said.
The MEK, whose leadership is based in Paris, said in a statement that six people were killed and more than 100 wounded.
The mortar fire struck Camp Liberty where residents from the MEK were moved last year, on Iraq's insistence, from their historic paramilitary camp of the 1980s -- Camp Ashraf, near the Iranian border.
One Iraqi security official said about 40 rockets and mortar rounds were fired into the camp, and the MEK gave a similar figure.
The United Nations said its special envoy Martin Kobler had asked Iraqi authorities to "promptly conduct an investigation into this," and added, "we have our monitors on the ground to follow up."
Eliana Nabaa, spokeswoman for the UN mission, said Iraqi officials had told the United Nations that "all those who were injured were hospitalised immediately."
UN High Commissioner for Refugees Antonio Guterres issued a statement condemning the attack.
"I call on the Iraqi government to do everything it can to guarantee security to the residents," he said. "The perpetrators must be found and brought to justice without delay."
Brussels joined in the condemnation.
"We condemn the attack of this morning ... and express our condolences to the families of the victims. We are concerned that it could add tension to the present situation in the camp," said a spokesman for EU foreign policy chief Catherine Ashton.
Camp Ashraf was the base that now-executed dictator Saddam Hussein allowed the group to establish in Diyala province in the 1980s, during Iraq's eight-year war with Iran.
The residents are in the process of being resettled, and a US official said in October that Washington and several European countries had agreed to take them in.
The MEK was founded in the 1960s to oppose the shah of Iran, and after the 1979 Islamic revolution that ousted him it took up arms against Iran's clerical rulers.
It says it has now laid down its arms and is working to overthrow the Islamic regime in Tehran by peaceful means.
Britain struck the group off its terror list in June 2008, followed by the European Union in 2009 and the United States in September 2012.
The US State Department holds the group responsible, however, for the deaths of Iranians as well as US soldiers and civilians from the 1970s into 2001, and in its note about delisting the MEK, stressed that it had not forgotten the group's militant past.
A senior US official also said at the time that Washington does "not see the MEK as a viable opposition."