"The Ayat Allah invoked his position that the planned transitional national assembly cannot represent the Iraqis in the ideal manner," said a statement released by Sistani's office after his latest meeting with a delegation from the US-appointed council.
"In this situation, experts think it is possible to organise fair and transparent elections in the coming months," the text said, restating Sistani's position.
Without an elected government, Sistani questioned Washington's right to negotiate a security agreement allowing US troops to stay in Iraq and the validity of a fundamental law to rule Iraq in the coming transition period.
Both documents "must be submitted to elected representatives of the people in order to have legitimacy."
Sistani warned the current plans for a provisional government "would create numerous problems."
The US-led coalition has ruled out early general elections on the grounds that Iraq's security situation is not stable and a national census still needs to be conducted.
"Ayat Allah Sistani insists on direct general elections," said Muwaffaq Rubaia, a Shia member of the council delegation which visited Sistani.
The team was headed by the council's president for January, Adnan Pachachi.
"We have a lot of respect for the Grand Ayatollah. We came to hear about his vision for the future of Iraq. We discussed the situation in the country," Pachachi, a Sunni Muslim, told reporters afterwards.
"Ayat Allah Sistani insists on direct general elections"
Shia member of the council delegation which visited Sistani
In November, Sistani came out publicly against US plans to transfer authority back to Iraq through the establishment of a transitional national assembly next May, selected by regional caucuses.
The assembly would then pick a provisional government to rule Iraq until general elections at the end of 2005.
The council has previously sent delegations to negotiate with Sistani, but the cleric, looked to for guidance by Iraq's 15-million Shia majority, has yet to budge on national elections.
Sistani has said he will consider dropping his demand if a team from the United Nations concludes it is impossible to organise a ballot.