The Post Office has confirmed that its current boss, Nick Read, is under investigation, after its former chairman Henry Staunton shocked MPs by making the revelation.
Mr Staunton was at a hearing to discuss compensation payments to sub-postmasters at the centre of the Horizon scandal.
Alan Bates, who inspired an ITV drama on the issue, told MPs the government should "get on and pay people".
The investigation is ongoing.
The Post Office confirmed there were complaints against Mr Read and other staff.
MPs were questioning a number of key figures about the pace of financial redress for thousands of sub-postmasters.
The MPs had been told by witnesses earlier in the day that an internal investigation was under way into Mr Staunton over his alleged behaviour while he chaired the company.
However, Mr Staunton alleged that there was actually an investigation into Mr Read.
He also claimed that within an 80-page document - a page of which he showed to MPs, with many lines redacted - it was said that Mr Read wanted to resign from the Post Office because he was unhappy with his pay.
The Post Office released a statement saying Nick Read "has never tendered his resignation and he continues to accept leadership responsibility for the challenges that we are all working on each day".
It added that there is "a complaint" against Mr Read and other employees, and that he "has cooperated fully with the investigation".
Why were hundreds of Post Office workers prosecuted?
The Department for Business and Trade said that it was aware that Mr Read was also under investigation but it had "not seen the 80-page report referred to by Henry Staunton and cannot attest to the content".
Downing Street has also insisted it has confidence in the Post Office boss, with the prime minister's deputy spokesperson saying: "We continue to work very closely with him.
"It's important at this point that everyone remains focused on ensuring we have the compensation and justice for the postmasters."
Some 700 sub-postmasters were prosecuted by the Post Office for theft and false accounting between 1999 and 2015 after the Horizon IT system, developed by Fujitsu, made it look like there were shortfalls at branch accounts.
It led to what has been described as the most widespread miscarriage of justice in British legal history.
Thousands more pumped their own money into the Post Office shops they managed to cover discrepancies caused by Horizon.
Sub-postmasters are seeking compensation from the government, but Mr Bates said the government - which owns the Post Office - has failed to get a grip on the process of paying money to claimants.
"It's very disappointing," he said. "This has been going on for years, as you well know, and I can't see any end to it."
Alan Bates speaking to reporters in Westminster on Tuesday
Mr Staunton, who was sacked as Post Office chair in January, said the compensation process had slowed right down until the Mr Bates vs The Post Office drama was aired in January and re-ignited interest in the long-running scandal.
The slow pace at which postmasters are receiving compensation risked being overshadowed by a recent row between Mr Staunton and Business Secretary Kemi Badenoch.
Mr Staunton gave an interview more than a week ago claiming that he had been told by a senior civil servant in January last year to slow down the spend on compensation.
Ms Badenoch hit back at the claims, saying they were "completely false". She also said she had sacked Mr Staunton following "very serious allegations about his conduct while chair of the Post Office". Concerns were also raised about the process of appointing a senior independent director at the Post Office, whose role includes challenging the chair on any issues. The appointment would replace Ben Tidswell, who is stepping down later this year.
Mr Staunton said on Tuesday that he was the victim of a "smear campaign", before he claimed that Mr Read was at the centre of an investigation, consisting of allegations made by the Post Office's former HR boss. Mr Staunton claims that Mr Read and the senior HR person "fell out".
The ex-chair also claimed that Mr Read had tried to resign four times during the time Mr Staunton was at the Post Office, between December 2022 and January 2024.
That contrasted with comments by Mr Read a short time earlier when, asked by MPs if he had ever tried to resign from the Post Office, he said under oath: "No. Why do you ask?"
The Department for Business and Trade said that Ms Badenoch "was clear in her statement to the House of Commons on 19 February that she lost confidence in Mr Staunton because he was blocking an investigation into his conduct, as well as his attempt to bypass the formal process to appoint a new director to the board".
It added: "The department will await the outcome of the investigation into Mr Read before making any further judgement."
However, speaking on BBC Radio 4's PM programme on Tuesday, Charlotte Nichols, a Labour MP who sits on the Commons Business committee, hit out at Ms Badenoch after the hearing.
"I think [Tuesday's hearing] really raises a number of questions for Kemi Badenoch, particularly as she came in quite characteristically two-footed in her denials of [Mr Staunton's] assertions when they were first made.
"I think that there are questions still to be answered about why recollections vary as much as they do," she added.