Ayat Allah Ali al-Sistani told senior UN official al-Akhdar al-Ibrahimi in a letter that unless the United Nations rejects the constitution, he would boycott a UN team expected to visit Iraq soon to advise on forming an interim government.
Al-Sistani, in a letter published by his office on Monday, said the United Nations should not approve the de facto constitution.
"The (Shia) religious establishment fears the occupation authorities will work to include this law in a new UN resolution to give it international legitimacy," he wrote.
"We warn that any such step will not be acceptable to the majority of Iraqis and will have dangerous consequences."
Al-Sistani wields great influence over Iraq's Shia community. His reservations held up the signing of the interim constitution for days. His latest objections could jeopardise the US handover deadline, or at least undermine the legitimacy of any Iraqi government that assumes power.
Under the interim constitution, direct elections for a transitional government, which will oversee the writing of a permanent constitution, must be held by January 2005.
"Consensus would not be reached unless there is pressure from a foreign power..."
Ayat Allah Ali al-Sistani,
In his letter, al-Sistani said the interim constitution was unworkable because it sets up a three-person presidential council, which he said would comprise a Sunni, a Kurd and a Shia. They would be required to take unanimous decisions.
"This builds a basis for sectarianism. Consensus would not be reached unless there is pressure from a foreign power, or a deadlock would be reached that destabilises the country and could lead to break-up," al-Sistani said.
Meanwhile, in continuing resistance violence, two visiting Finnish business people were shot dead as they drove through a tunnel in Baghdad on Monday.
Separately, an Iraqi security guard was shot dead and three others wounded in the northern city of Mosul as they walked to work, Iraqi security officials said. A civilian was also wounded.
A car bomb wounded eight members of the paramilitary Iraqi Civil Defence Corps outside a US military base north of Baghdad, the US occupation military said. Only the bomber was killed.
In other violence, 13 British soldiers were wounded in blasts in the southern Iraqi city of Basra, the British Defence Ministry said. None of the injuries was thought to be life-threatening.