The splits emerged ahead of an Organisation of Islamic Conference (OIC) summit, which opened in Malaysia on Monday.
Thirty five heads of state or government are attending the meeting, making it the largest gathering of Muslim leaders since the 11 September 2001 attacks on the United States.
Malaysia denounced the US-led occupation of Iraq on Monday, as well as Israel's treatment of Palestinians, saying they represented a threat to "the very survival" of the worldwide Muslim community.
Malaysian foreign minister, Sayid Hamid Albar, said full sovereignty should be returned to Iraq, as well as control over its oil.
"Foreign occupation of Iraq today is a reality (as is) the existence of the provisional Governing Council," he said.
"However, foreign occupation of the country must be brought to an end as soon as possible. ... It is our moral duty to assist the people of Iraq to regain their sovereignty and integrity."
However, Iraq's US-appointed foreign minister said Muslim nations needed to accept the reality that American troops would remain for a while, and told them to help the country's recovery by contributing peacekeeping forces and money.
Hushyar Zebari said he had urged countries attending the OIC summit to contribute Muslim forces to help bring the security situation under control.
Zebari said Muslim nations should
send peacekeepers to Iraq
But the indications were not encouraging, he said.
"I don't think there is any desire by the Muslim countries to send troops. I mean, that's the feeling I'm getting from my initial contacts."
At the outset of the weeklong meetings on Saturday, senior officials from the 57 members of the OIC urged the "eviction" of US troops from Iraq - something Zebari said would not happen in the near future.
"Yes, legally under international law there is an occupying power controlling Iraq... and they (Muslim countries) want this state of affairs to be ended as soon as possible, and we share this view, but we believe this needs to be done in a gradual way," Zebari said.
"Nobody should question the Iraqi people's willingness and desire to regain their sovereignty and full independence, but we understand at the same time it's not easy, it's a complicated issue."
Turkey is the only Muslim country so far that has agreed to send troops to help the United States stabilise Iraq, where its troops are under daily attack.
Pakistani Foreign Minister, Khurshid Mahmud Kasuri, said on Monday that Pakistan would send troops if it had a UN mandate, was part of a multilateral Muslim force, or received an Iraqi request that would ensure the troops were welcome.
Kasuri said it was unrealistic to demand that the United States should pull out, as it was unlikely other nations had the capacity to stabilise the country without US troops there too.
"Nobody's asked for that, neither France, nor Germany. People are not so unrealistic," Kasuri said.
"After all the US has 150,000 troops (in Iraq). Who's going to come up with that?"