Khatami, reformist head of state from 1997 to 2005, and his predecessor, Akbar Hashemi Rafsanjani, moderate president from 1989 to 1997, have yet to decide whether to contest the polls to succeed Mahmud Ahmadinejad.
But Intelligence Minister Heydar Moslehi has warned the pair, without naming them, over their alleged role in the protest movement that followed Iran's disputed 2009 election.
In a statement published on his personal website and reprinted today by the English-language Tehran Times, Khatami said his candidacy -- which may be rejected -- could aggravate tensions with the authorities and harm the reformist movement.
He was referring to the two reformist candidates from the 2009 election, Mehdi Karroubi and Mir Hossein Mousavi, who charged the election results were fraudulent, and the latter's wife, who are under house arrest.
"We are in a situation where the election mechanism is flawed," the ex-president said.
"There are people standing against us who prefer another trend, and if someone criticises that trend and mull over a better path for the society and the country, they do not allow him to have a presence," he said.
Candidate registration opened on Tuesday and will close on Saturday.
The process of screening candidates is entrusted to the Guardians Council, an unelected body controlled by religious conservatives named by the Islamic republic's supreme leader Ayatollah Ali Khamenei.
The council is set to announce the names of those who have been cleared to stand by May 23 and successful candidates will have three weeks to campaign ahead of the elections.
Incumbent Ahmadinejad can not run for a third term.
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