The provincial governors, who are responsible for administering the elections in their areas, have said they will resign in a week if what they call the conditions for a free and fair election are not met.
The governors are appointed by the interior ministry which says it will not take account of the disqualifications.
Authority
Mr Khatami is expected to confer with the country's supreme leader, Ayatollah Ali Khamenei, and Parliamentary Speaker Mehdi Karroubi, to try to defuse the crisis.
It is to Ayatollah Khamenei that all eyes are now turning as this crisis deepens, our correspondent says: only he has the authority to step and adjudicate.
Mr Khatami says he is trying to avert a crisis
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The 12-member Council of Guardians, made up of six clerics and six Islamic lawyers, is empowered to ensure parliament's actions comply with Islamic principles.
It is expected that the council would requalify a number of the blocked candidates on appeal, our correspondent adds.
Council spokesman Mohammad Jahromi said 2,033 of the 8,200 candidates had been barred but MPs said the figure was higher.
MP Reza Yousefian said more than 80 of 290 MPs had been banned from re-election.
Iran's parliament is dominated by the reformists who have won all major national elections since 1997.