The criticism from Ayat Allah Ali al-Husayni al-Sistani devalued a lavish ceremony to mark the signing of the charter by the US-picked Iraqi Governing Council.
"Any law prepared for the transitional period will not gain legitimacy except after it is endorsed by an elected national assembly," al-Sistani said in a statement.
He added that "the adoption of this law marks a historic milestone in the Iraqi people's long journey from tyranny and violence to liberty and peace. While difficult work remains to establish democracy in Iraq, today's (Monday) signing is a critical step in that direction."
Al-Sistani supporters on the IGC pledged to try and amend parts of the 22-page charter.
Most of the council's 13 Shia members refused to sign the document on Friday, citing al-Sistani's opposition for their last-minute decision.
Shia objections centred on a clause on a referendum due to be held next year to approve a permanent constitution once it had been drawn up.
The clause states that even if a majority of Iraqis approves the constitution, it can be vetoed if two-thirds of voters in three provinces reject it. This specific clause was inserted by the Kurds who run three provinces in northern Iraq and want to be able to veto any attempt to rein in their considerable autonomy.
Kurds have demonstrated for
some kind of autonomy in Iraq
Another objection involved the make-up of a presidential council.
Currently the document calls for the creation of a three-member council, with one president and two deputies. The Shia have said they want a five-person council, with three Shia, one Sunni and one Kurd.
Turkey also voiced unhappiness over the interim constitution, warning it would pave the way for more instability in the country.
"The interim law does not satisfy us, it increases our concerns," Anatolia news agency quoted Justice Minister Cemil Cicek, as saying.
But Cicek said Turkey saw the constitution "as an arrangement that will not help the establishment of permanent peace in Iraq and one that will allow for the continuation for a long time of unrest and instability there."
"The interim law does not satisfy us, it increases our concerns"
Justice Minister, Turkey
He did not specify which provisions Turkey disliked.
Ankara has repeatedly warned against moves in post-war Iraq that could help the Iraqi Kurds enhance their self-rule in the north of the country.
It fears increased political influence for the Iraqi Kurds could set an example for their restive cousins in adjoining southeast Turkey, where a bloody Kurdish rebellion had only recently been subdued.
Under the constitution, Iraqi Kurdistan will retain its federal status and the rest of Iraq will be given the right to prepare to form states.