Deputy Prime Minister Hussain al-Shahristani said Qatar's welcoming of Vice President Tariq al-Hashimi was "unacceptable."
Hashimi is the top Sunni official in Iraq's Shiite-led government.
His trip to Sunni-led Qatar could deepen tensions between Iraq and the Sunni monarchies in the Persian Gulf.
Hashimi fled to Iraq's semiautonomous Kurdistan region after the Iraqi government in December accused him of running death squads against Shi'a.
The government asked Kurdish regional authorities to hand him over but they declined.
Hashimi arrived in Qatar on April 1 and was greeted by a minister of state, Sheikh Hamad bin Nasser bin Jassim al-Thania, a member of Qatar's ruling royal family.