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.
The group that complained on Sunday, the Guardian Council, also vets all candidates for the presidency. Mashaei is among more than 680 hopefuls, but no more than a handful will be selected for the final ballot.
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.
The Council's members said that public fund rules were broken when Ahmadinejad accompanied Mashaei to the election registration office on Saturday, said Kadkhodaei.
A conviction could bring a maximum punishment of six months in jail or 74 lashes. Kadkhodaei did not elaborate.
Ahmadinejad has strongly pushed Mashaei as his political heir, but there are serious obstacles to his protege making the final ballot. As part of Ahmadinejad's disputes with the ruling clerics, Mashaei has been denounced by hard-liners as leader of a "deviant current" that seeks to undermine Islamic rule.
Mashaei has long been Ahmadinejad's close confidant, and the president's son is married to Mashaei's daughter. State TV on Saturday 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.
So far, the slate in the race for the June 14 vote is almost certainly to be heavily stacked with those considered loyal to the Supreme Leader Ayatollah Ali Khamenei, who has been angered by challenges to his authority by Ahmadinejad and the president's allies.
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 Saturday, 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 Saturday came just hours after the deadline to register for the June 14 race expired.
Mehmanparast will be replaced by Abbas Araghchi, a member of Iran's nuclear negotiators team, the Mehr agency reported. Araghchi would also continue his current job as deputy foreign minister in charge of Asia and Oceania.
The British-educated Araghchi, 50, served as Iran's ambassador to Japan in 2008-11.