Hundreds of ministry employees had gathered at the Abu Hanifa mosque in Baghdad to elect four new directors general, part of attempts by the United States and Britain to slowly introduce more democracy following the fall of Saddam Hussein.
But it was decided to delay the vote after complaints from ministry officials, most of whom are preachers at mosques.
Employees said a Shi'ite cleric had complained there were not enough Shi'ite candidates. Most Iraqis are Shi'ite, but Saddam Hussein's deposed government was dominated by Sunnis.
Other clerics said the candidates included too many people who used to run the ministry during Saddam's rule.
''We completely reject these elections because the same faces who used to run the ministry have put their names forward. We want new people to run the ministry,'' said Sheikh Zaid al- Summadai, preacher at Baghdad's Um al-Tubul mosque.
But organisers of the elections said senior Baath Party members and former directors general were not allowed to stand.
''The elected directors general will not be Baathists. We expect them to be men or women of honesty, integrity and character,'' said Stephen Browning, the U.S. senior adviser to the ministries of health and endowment and religious affairs, who attended the gathering.
Browning said the U.S.-led administration would soon convene a meeting that would be attended by more than 35 respected religious leaders -- Sunni, Shi'ite, Turkmen, Christian and Kurds -- to choose five to seven clerics who would form an executive committee for the ministry.
''The committee will essentially run the ministry of religious affairs and endowment and the directors general will be responsible for the implementation of the policy set by the executive committee,'' he said.
It was not immediately clear when the delayed elections for the new directors general might be held.