Adil al-Lami, a commisson official, said: "A court has overruled the commission's initial decision to allow them to run and we are now applying the law and removing the names of about 100 candidates.
"We are asking political parties to submit new names from the same electoral lists to replace the candidates struck off."
He gave no details about which parties and candidates were affected.
The electoral law does not allow former senior officials from the Baath party to run for parliament. Final election results are not expected before January.
Most of those struck off are believed to be Sunni Arabs who were dominant under Saddam Hussein, the former president.
While the disqualifications should not affect the parties' overall parliamentary representation, they are expected to lead to the exclusion of some prominent figures.
Investigations and unity
Robert Ford, a senior US diplomat in Baghdad, said on Friday that Washington hoped that the new Iraqi government would help to foster national unity.
The US was hoping to see "a government that fosters a sense of national reconciliation, holding to account criminals of the last regime when necessary, but in general working towards national reconciliation".
Al-Lami said: "The electoral commission is investigating 1500 complaints arising out of the election, including at least 20 serious allegations."
"If need be, the vote can be repeated in small areas"
electoral commisson official
But complaints concerned no more than 5% of the total of 10 million votes cast, he said.
About two dozen parties, including the main Sunni Arab coalition, called on Thursday for a re-run of the elections because of alleged fraud.
Al-Lami said: "If need be, the vote can be repeated in small areas, but there is no evidence until now this will be required."