The Palestinian Football Association accuses Israel of obstructing its activities and restricting the movement of players between the Gaza Strip and the Israeli-occupied West Bank. It wants a vote on Israel's suspension from FIFA at a congress on May 29.
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"The Israeli federation is behaving as a part of the brutal, racist occupation," Jibril Rajoub, a former politician who has headed the PFA since 2008, told reporters in the West Bank.
"The Israeli Football Association is not innocent ... The Israel FA has failed to take a stance against its government's policy to hinder the development of Palestinian football."
If FIFA were to suspend Israel, its teams and clubs would be barred from international events, including World Cup qualifications.
Although suspensions are not uncommon, FIFA has usually taken such action only when a government is deemed to have intervened in its soccer association's affairs.
On Wednesday, Israel's top soccer administrators met FIFA President Sepp Blatter in Zurich to try to avert the vote.
Afterwards, FIFA said Blatter had "reiterated his position that any member association that is fulfilling its statutory duties should not be suspended... This would also apply to the IFA as long as they fulfil such duties."
The statement appeared to offer hope for the IFA, which has not been accused of violating FIFA statutes and argues that it cannot influence Israel's security forces.
FIFA said it would host a meeting between IFA chairman Ofer Eini and Rajoub in the coming days. Rajoub said Blatter had called him urge him to meet his Israeli counterparts but he had not yet decided whether he would do so.
In the past, Blatter or his envoys have managed to broker compromises between the Israelis and the Palestinians, but this time Rajoub said he was not interested in a "private deal".
"We are committed to the statues of FIFA, we are committed to the principles, but at the same time we are committed to go for the resolution in the congress of FIFA," he said. "There is no compromise, there will be no private deal."
As well as restrictions on the movement of players, Rajoub accuses Israel's FA of turning a blind eye to racism against Arabs in Israeli football and says five Israeli league teams based on Jewish settlements built on occupied land should not be allowed to play.
The PFA has also complained about equipment ordered by the PFA being held up at Israeli customs. Israel says its actions are guided by security concerns.
In a letter to FIFA members, IFA chairman Eini urged them to reject the Palestinian proposal, saying it was "a flagrant move that seeks to mix politics with sport - something that is completely contrary to FIFA's vision".
The Palestinian proposal would need the approval of 75 percent of FIFA's 209 member associations.
Israel is competing in the Euro 2016 qualifying event and its clubs will join European cup tournaments in July, when Israel is also due to host the European women's under-19 championships. Suspension could force the event to be moved.
Two years ago, FIFA set up a task force which included Blatter, the Israeli and Palestinian FA chiefs and the heads of the European and Asian confederations to address the Palestinian complaints.
Eini's letter to FIFA members said that last year, Blatter appointed Cyprus FA president, Costakis Koutsokoumnis, to go to the region to gather information. He wrote that Koutsokoumnis reported that the IFA was not involved in determining Israeli travel policy and that FIFA, together with the IFA and the PFA, should try to help guide Israeli security agencies' procedures to ease the situation.