"Ahmadinejad is not complying with the will of the people," the Financial Times Deutschland quoted Grand Ayatollah Bajat Sanjani as saying. "This is a major threat, a big danger," he added in an unusually direct personal attack.
The newspaper also said Sanjani accused Ahmadinejad's government of breaking the law, seriously encroaching on existing freedoms and illegally empowering the Revolutionary Guard.
Ahmadinejad is expected to seek a second term in next year's presidential election.
He has faced mounting criticism from the public and opponents who back reform, particularly over his handling of the economy and rising inflation which has hit about 26 percent. Price rises are the biggest gripe for many ordinary Iranians.
But Iran's supreme leader has told Ahmadinejad to prepare for a second four-year term, according to media.
Sanjani urged prominent reformers to unite before the election.
(Reporting by Madeline Chambers)