"Following an insulting speech made in a ceremony by Mr Sanei against the president, the president's legal office has prepared a complaint against him," Fars said, quoting an unnamed source in the presidential office.
"The complaint will be submitted to the Special Court for Clergy," the source said, without offering further details.
In August, hardline newspaper Javan accused Sanei of calling Ahmadinejad a "bastard" in comments made among his supporters but the cleric's office denied the report.
Sanei is a respected Shiite "source of emulation" and is based in the religious city of Qom with many followers across Iran and abroad.
Known for his progressive fatwas, especially on women's rights, he is also a vocal supporter of Iran's opposition which has rejected Ahmadinejad's re-election as fraudulent.
Ahmadinejad has had a tough time with Iran's clerical elite and most senior ayatollahs have refused to congratulate him on his re-election.
