The website quoted "well informed sources" as saying that Khatami had been told he could not travel by the Iranian government.
The AFP news agency quoted a different source who said that the "police warned Khatami he could not leave the country."
'Advised' to stay
But a lawyer representing the former president, a vocal opponant of the Iranian regime, said that there was no travel ban in place and that he had only been "advised" to abandon his trip by government officials.
"No order was given prohibiting Khatami from leaving the country," Mahmoud Alizadeh Tabatabie said.
"The cancellation of his visit to Japan was decided following the advice of certain (government) bodies and there has been no decision to ban Khatami from leaving the country."
Khatami had been invited to attend the conference, which is being held in the Japanese city of Hiroshima.
The former Swedish and Canadian Prime Ministers have issued a statement of protest from the summit, calling for President Mahmoud Ahmadinejad to lift the travel restrictions.
"We strongly protest this restriction on his freedom,'' the two former prime ministers said.
"International dialogue and mutual learning is especially critical on the crucial subject of nuclear disarmament because Iran is such a prominent participant in this debate.''
Khatami has come in for heavy criticism from the Iranian government since backing opposition presidential candidate Mir Hossein Mousavi in last year's disputed election.
He has since called for the release of hundreds of opposition demonstrators being held for taking part in protests against the government.
The former president has criticised the government's treatment of opposition supporters since concerns over the integrity of the vote brought thousands of protesters onto the streets last summer.