The dispute appears to stem from an ongoing confrontation between Ahmadinejad and the ruling clerics in Iran following years of tensions over power struggles.
It could also herald potential difficulties for Ahmadinejad's protege, Esfandiar Rahim Mashaei, to be cleared for the June 14 presidential election, which is to pick Ahmadinejad's successor.
The president himself is not running since Iran's constitution bars him from seeking a third term in office.
State TV quoted Guardian Council spokesman Abbas Ali Kadkhodaei as saying the claims against Ahmadinejad will be referred to the country's judiciary for possible charges.
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The Council's members said that public fund rules were broken when Ahmadinejad accompanied Mashaei to the election registration office yesterday, said Kadkhodaei.
A conviction could bring a maximum punishment of six months in jail or 74 lashes. Kadkhodaei did not elaborate.
Mashaei has long been Ahmadinejad's close confidant, and the president's son is married to Mashaei's daughter. State TV yesterday showed a smiling Ahmadinejad accompanying Mashaei as he submitted his papers at the registry office, and the president raised his aide's hand in a gesture of support.
Ahmadinejad's opponents have repeatedly accused him of using any opportunity and public funds for promoting Mashaei.
Among the presumed front-runners is senior Khamenei adviser Ali Akbar Velayati, Tehran Mayor Mohammad Bagher Qalibaf, prominent lawmaker Hadad Adel and top nuclear negotiator Saeed Jalili.
Also yesterday, a powerful and divisive figure registered to run Akbar Hashemi Rafsanjani, a former president who still wields enormous influence.
In other election-related developments, Iran's foreign ministry spokesman has stepped down after joining the race. A report by the semiofficial Mehr news agency said Ramin Mehmanparast resigned from the post. It gave no reason, but the report late yesterday came just hours after the deadline to register for the June 14 race expired.
The British-educated Araghchi, 50, served as Iran's ambassador to Japan in 2008-11.