Gianni Infantino, the Fifa president, was under investigation by the organisation’s ethics committee for more than one separate alleged instance of malpractice when he organised the sudden removal of the committee chairmen and members last month.

The Guardian has learned that the Swiss prosecutor Cornel Borbély, who was chairman of the ethics committee’s “investigatory chamber”, had begun examining complaints that Infantino and the Fifa general secretary, Fatma Samoura, improperly sought to influence the election in March of their favoured candidate for president of the Confederation of African Football (CAF), Ahmad Ahmad .

The allegations are understood to include claims from senior figures in African football that Infantino and Samoura promised FA presidents, in a series of private meetings, that they could accelerate the payment of Fifa development money to their football associations if the presidents voted for Ahmad.

Infantino is said to have manoeuvred for the ousting of the longstanding CAF president, Issa Hayatou, because Hayatou did not support him in the Fifa presidential election last year, instead endorsing the rival candidate, Sheikh Salman bin Ibrahim al-Khalifa of Bahrain.

Borbély is also understood to have been in the early stages of an investigation into a further possible ethics breach by Infantino.

Infantino’s opportunity to claim the highest office in football administration landed because the ethics committee in December 2015 banned the previous Fifa president, Sepp Blatter, and the favourite to succeed him, the then Uefa president Michel Platini, for malpractice.

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Infantino, Uefa’s general secretary at the time, threw himself relentlessly into his campaign to become president instead, making a central promise to provide much more money to national football associations, and flying repeatedly around the world, including by private jet, to assure voting FA presidents of his credentials. Infantino declared publicly that he had been supported by Uefa with €500,000 (£438,000) to support his Fifa presidential election campaign. Uefa is understood to have doubled that first instalment, committing to pay two further instalments of €250,000.

After he was elected president in February 2016, Infantino was cleared of ethics breaches following an investigation relating mainly to his acceptance of two private jet flights, but some Fifa sources have said he was furious and indignant at being investigated at all.

At the Fifa congress in Bahrain last month, neither Borbély nor Hans-Joachim Eckert, the former German judge who chaired the ethics committee’s “adjudicatory chamber”, which assesses the investigations and decides on sanctions, were given any notice that their four-year terms were not going to be renewed.

Questions still remain over the way this was done: it appears that Infantino himself first asked football’s six confederation presidents to recommend appointees. Then, two days before the congress, he and Samoura presented the list of names, without Borbély or Eckert on it, to the 36-person Fifa council which is responsible for formally proposing independent committee chairs to the congress.

Uefa sources have said that they did, as requested, suggest new names for possible membership of the committees, but not for specific positions, and they were not involved in the decision to end Borbély and Eckert’s chairmanship.

The council members, including the English FA and Uefa representative David Gill, formerly Manchester United’s chief executive, who are paid $300,000 (£235,000) annually plus daily allowances for attending meetings, approved the non‑renewal of Eckert and Borbély apparently without asking any questions. Gill said at the time that the new appointees had good credentials, and there was no automatic right for the serving chairmen to have their terms renewed.

Eckert and Borbély responded indignantly, saying that they had been working on “hundreds of cases” of potential Fifa‑related malpractice which would now be set back. They argued that their removal “incapacitated” and “neutralised” the integrity of the whole semi-independent reform process introduced after Fifa was brought to near collapse last year by multiple corruption scandals. Infantino responded at the Congress by questioning the two men’s efficacy, and denounced “fake news” and alleged “Fifa bashing”.

The investigations into Infantino are now said to have stalled and in effect stopped. Borbély is known to have followed up the complaints of the African football administrators and scheduled to meet at least one of them in Zurich last week. But after Borbély’s sacking, that witness is understood to have been told by Fifa not to go.

Borbély is also understood to have begun an investigation into the newly elected CAF president, Ahmad, for allegedly seeking money from the former Asian Football Confederation president, Mohammed bin Hammam, who was banned by Fifa in 2012. Ahmad has denied wrongdoing.

Further details have also emerged about the intense internal pressure put on Miguel Maduro, chairman of the governance committee, another in Fifa’s new supposedly independent structure, before he too was fired at the Bahrain congress. Maduro, director of the global governance programme at the European University Institute in Florence, had been the committee chairman for only eight months. After he was fired, three members of the governance committee, Joseph Weiler, Ron Popper and Navi Pillay – distinguished experts recruited to give the reforms credibility – resigned in protest.

A key decision thought to have led to toxic resentment of Maduro exercising his duties independently, was his committee’s ruling that Vitaly Mutko, Russia’s deputy prime minister, was not eligible to be a member of the Fifa council, due to the rules requiring separation of Fifa from national politics. Infantino himself is said by Fifa sources to have told Maduro that the ruling on Mutko was very difficult for him and Fifa, given Russia’s hosting of the World Cup next year, and the Russian oil company Gazprom’s sponsorship.

Maduro is also understood to have come under sustained pressure from within Fifa when he declined eligibility for the Fifa council to the Qatari football official Saoud al-Mohannadi, who was charged with ethics breaches. Fifa is dependent on Qatar both for the hosting of the 2022 World Cup and, since May, for the sponsorship by Qatar Airways. Maduro’s initial ban on Mohannadi was said by Fifa sources to have been strongly resisted. Mohannadi was reinstated in April after a successful appeal against his ethics charges.

Maduro has not since discussed the specific cases on which he worked, but he confirmed to the Guardian that he did face severe resistance and pressure within Fifa, despite his position being independent. He said he found his sudden removal in Bahrain shocking, concluding that it was motivated by the ambitions and political manoeuvring of senior Fifa figures, and breached the independence principle underpinning the reforms. The Fifa council members are understood not to have questioned Maduro’s replacement.

“I am now convinced that only outside pressure, perhaps from the US authorities or the European Union, can secure meaningful reform of Fifa,” Maduro said. “Without it, Fifa won’t reform; its problem is systemic. The fundamental problem is that the power is really important to people within Fifa, so they have a problem accepting independent governance and scrutiny.

“If you have such a systemic problem, then this is an environment for corruption to emerge.”

Borbély was replaced by María Claudia Rojas, a lawyer in Colombia; Eckert by Vassilios Skouris, a former president of the European court of justice; Maduro by his former deputy, Mukul Mudgal, a former senior high court judge in India. Fifa has explained the replacements by saying the intention was to “better reflect the geographic and gender diversity” of an international organisation – even though Skouris is a male European like Eckert.

Most prominent among the hundreds of files Borbély and Eckert were working on were the extensive allegations of malpractice by German football officials during their bid to host the 2006 World Cup. One of their concerns is the complexity of that case, involving analysing evidence in thousands of documents in German, which will now have to be translated for Rojas.

The Guardian has been told that since Borbély’s removal, there has not been a professional handover and transition process to Rojas, hence the suspension of the ongoing investigations. A Fifa spokesperson, however, said the transition is starting.

“We can confirm that both chairpersons are fully onboard with the activities of the committee and therefore it is operational and work is ongoing,” the spokesperson said. “The new chairpersons met at the end of May in Zurich and a transition plan was laid down and is currently under implementation.”

Fifa said that correct procedures had been followed when the nominations for committee appointments were made by the regional confederations, then presented to the Fifa council. The spokesperson said that the new chairs are experienced and expert.

Responding to the revelation that Infantino himself was under two investigations at the time Borbély and Eckert were removed, Fifa said: “We will not comment on baseless speculations, which are unfortunately put forward only for ill-intended purposes.”