Fifa president Gianni Infantino tried to influence the decision to block Russian World Cup official Vitaly Mutko from keeping his seat on football's ruling council, MPs have been told.
Miguel Maduro, the ousted former chair of Fifa's governance committee, said Infantino "expressed concern" about the impact on the 2018 World Cup.
Maduro said Fifa general secretary Fatma Samoura warned him to "find a solution or the presidency would be in question and the World Cup would be a disaster".
In March, Mutko was successfully barred because his role as Russia's deputy prime minister was deemed to be in conflict with Fifa's regulations on political neutrality.
But Maduro was dismissed in May after less than a year with football's governing body.
He said Infantino "was not comfortable" with the ruling against Mutko, and also believed there was "no evidence" Mutko is involved in Russian doping.
In a statement, Fifa called Maduro's allegations "factually incorrect", adding: "The independence of Fifa's committees and the success of Fifa's reform process will only be measured by the decisions taken in the future and not by personal opinions."
A former government minister in Portugal, Maduro had been hired to help boost Fifa's image following several corruption scandals.
Infantino praised his appointment in 2016, pointing to his reputation as a sign the organisation he leads was serious about reform.
But Maduro told the Culture, Media and Sport Select Committee at the House of Commons that Fifa has an "incapacity" to deal with independent scrutiny.
"There is a culture in the institution itself that is extremely resistant to accountability," he said.
He said Infantino chose to "politically survive" rather than protect independent bodies, and stopped speaking to him after the Mutko issue.
Maduro also alleged:
- Fifa has a culture of governance that is "a system of rules without the rule of law".
- Without "systemic culture changes", things will stay the same.
- Some confederations tried to block full implementation of new rules on electing female committee members.
- Half of the governance committee are currently not independent, as required.
- In elections, different coloured pens could be distributed to identify how people vote.
- Egypt's Fifa member (Hany Abo Rida) threw a party and flew in delegates after being re-elected in May
Maduro unexpectedly left Fifa along with Cornel Borbely and Hans-Joachim Eckert, the heads of its ethics investigatory and adjudication bodies.
Fifa said at the time it wanted to "better reflect the geographic and gender diversity that must be a part of an international organisation".
Select committee chair Damian Collins told Wednesday's hearing Borbely was stopped by Fifa from giving evidence to MPs.
"To say he is prevented from speaking is in itself extremely surprising in the least. What is more revealing is the answer was supplied by the secretary general," said Maduro.
Fifa is also facing an ethics complaint filed by Joseph Weiler, a New York University professor who was one of several independent members of Fifa's governance panel who quit in May in protest at Maduro's removal.
Weiler filed the complaint against Fifa's top leaders, including Infantino, this week and it's understood to include the series of claims made by Maduro on Wednesday.
The session will form part of the committee's ongoing inquiry into sports governance. A final report is due to be published later in the autumn.
Richard Conway, BBC sports news correspondent
Maduro's appointment was billed by Fifa as a sign it was serious about reform.
His credentials were impeccable - a respected politician at home in Portugal and a former advocate general of the European Court of Justice.
And yet, within a year, he was dumped out of the organisation.
Much hope was pinned on Infantino implementing true transparency and accountability following years of decisions made in smoke-filled rooms.
If Maduro is to be believed then not much appears to have changed. He asserts it will take external pressure, possibly from the EU, to shake things up given structural faultlines which inevitably place political necessity ahead of independent decision making.