"Hundreds" of cases of alleged wrongdoing - some involving senior officials - were being looked into by Fifa's ethics committee before its main investigator and judge were ousted, the two have claimed.
Football's world governing announced on Tuesday it will not reappoint investigator Cornel Borbely and ethics adjudicator Hans-Joachim Eckert.
At a news conference on Wednesday, they said their removal was a "setback for the fight against corruption" with knowledge of the cases being lost.
The pair had earlier said it "meant the de facto end of Fifa's reform efforts".
Borbely believes his removal was politically motivated.
"We investigated several hundred cases and several hundred are still pending and ongoing at the moment," Swiss Borbely said on Wednesday.
He also outlined how he believed his removal along with German judge Eckert was "not in Fifa's best interests and against good governance".
It "weakened and incapacitated" football's world governing body, adding that "Fifa's code of ethics is a dead letter".
World football's governing body launched a reform process following the arrests and indictment of several officials on bribery and corruption charges in 2015.
Borbely and Eckert have combined to ban numerous football officials in that time.
Last year the committee investigated - and cleared - Fifa president Gianni Infantino of wrongdoing related to his expenses and sacking of whistleblowers.
Eckert's tenure has not been without criticism, however. In 2014 his report which cleared Russia and Qatar of corruption in the 2018 and 2022 World Cup bids was described as "erroneous and incomplete" by Michael Garcia, who had spent two years investigating the claims for Fifa.
Borbely and Eckert will be replaced by Colombian prosecutor Maria Claudia Rojas and Greek judge Vassilios Skouris, who was head of the European Court of Justice for 12 years until 2015.
How has Fifa responded?
Fifa released a statement on Wednesday in response to the claims of Borbely and Eckert, saying that they wanted to "better reflect the geographic and gender diversity that must be a part of an international organisation like Fifa".
One senior Fifa official had previously said the pair are guilty of "hype".
"It's not like we replaced them with non-independent people," Fifa vice president Victor Montagliani told BBC Radio 5 live sports news correspondent Richard Conway.
"They were replaced by two independent people of very high quality and standards. And so with all due respect, and they may be disappointed that they wanted to continue in the role, there's a lot of chairmen of a lot of other committees that want to continue as well. But at the end of the day Fifa and any other organisation has the right to change people on the committees."
Montagliani added the decision to replace them was "absolutely not" politically motivated - and suggested the two had made it political by speaking out.
"It's been way overblown from a hype perspective. I'm a little uncomfortable when judges start speaking in the media, either during their tenureship or even after their tenureship. I think that is quite unprofessional," he continued.
"The work needs to be done in a very humble way.
"From a public standpoint these committees need to do their work, and quietly do their work, efficiently, judiciously and execute it. They've both done a very good job, they've done yeoman's work in terms of what they've done, a lot of hard work. I take my hat off to them but I think it's time to give someone else an opportunity."
Fifa council member Sunil Gulati refused to expand on why the council did not want the two to continue in their role when asked by BBC World Service's Mani Djazmi, but added: "I have great respect for them and think they are outstanding legal minds. The people that have been asked to step into these roles are very high quality."