Mahmoud Doaei of the moderate Ettelaat daily used an image of Khatami on Saturday, also translating remarks that the politician made in an interview with Lebanon's As-Safir newspaper.
The indictment from a media court urged that Doaei, a cleric, be put on trial for breaking an order of Tehran's prosecutor that neither Khatami's picture nor comments be used.
Iran's judiciary news service quoted an informed official as saying the reporting ban was still in force and "press and media violating the order will be dealt with according to the law".
Legal authorities have barred reports involving officials described as "heads of the sedition", a reference to deadly protests after Iran's disputed presidential vote in 2009 in which Mahmoud Ahmadinejad was re-elected.
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Khatami, president between 1997 and 2005 and whose tenure was marked by unsuccessful attempts to open up Iran to the West, was among prominent figures who said the ballot was fraudulent.
He refused to recognise Ahmadinejad's re-election, echoing claims by reformist opposition leaders Mir Hossein Mousavi and Mehdi Karroubi that the vote was rigged.
Mousavi and Karroubi, who ran against Ahmadinejad, have been under house arrest since February 2011.
Khatami repeatedly called for the release of Mousavi and Karroubi but following the ban on his name and picture he is only referred to as "head of the reformist government" in the media.
The former president has more or less vanished from public view as a consequence. Iranian authorities temporarily blocked two websites in February for publishing reports and pictures of him.
Iran's current President, Hassan Rouhani, who took office in 2013 on the platform of more social and political freedom, said before being elected that he hoped restriction on Mousavi and Karroub would end. But no such action has been taken.