Former MP says questions about credit card spending were intended to scupper chances of becoming police commissioner

The Cabinet Office has been asked to investigate claims that key parts of a letter written to Lord Prescott by the country's most senior civil servant were removed without authorisation.

Lord O'Donnell, who was head of the Cabinet Office, has asked his successor, Sir Jeremy Heywood, to investigate why a crucial paragraph from his letter to the former deputy prime minister was removed and by whom.

Its removal is part of a sequence of events that Prescott claims amount to a "dirty tricks" campaign against him, including what he alleges were planted parliamentary questions that have been mysteriously misreported in Hansard. Prescott claims the questions about spending on Whitehall credit cards during his time in office were part of a Tory campaign to scupper his chances of becoming a police commissioner.

The questions triggered newspaper stories conveying the impression that Prescott enjoyed hospitality at taxpayers' expense when he was deputy prime minister and prompted the local government minister, Grant Shapps, to claim: "Prezza seems to have a cavalier attitude to the public purse."

But, in a letter to Prescott last year, O'Donnell confirmed that the former deputy prime minister never had a credit card and his officials used departmental cards appropriately. O'Donnell's letter was copied to the Department for Communities and Local Government, which published the figures revealing spending on department credit cards during Prescott's time in office.

The Observer has established that in a first draft of the letter – dated 18 November 2011 and addressed "Dear John" and signed "Yours ever, Gus" – O'Donnell said he had warned department staff that former ministers such as Prescott must be informed when Whitehall departments publish information about them. This protocol allows former ministers to prepare a response to allegations raised about them in parliament.

The reference to the warning was removed from the version of the letter sent by the Cabinet Office to Prescott, with the date changed to 22 November 2011 and O'Donnell's personalised greeting and signoff removed.

A spokesman for the Cabinet Office said the changes to the letter were made by the department. The Observer understands that O'Donnell was never made aware of the changes.

Prescott has written to Heywood, asking him to find out who altered the letter and why. Prescott believes the paragraph was removed by someone within the department as part of a campaign to scupper his chances of becoming a police commissioner, a claim denied by officials.

It also appears some of the parliamentary questions about use of procurement cards under Prescott were tabled by MPs who never made them.

The Lib Dem, Sir Alan Beith, was credited in Hansard with asking a question in April relating to Prescott's use of procurement cards but it later transpired the question was asked by the Tory MP for Dover, Charlie Elphicke. A question asked by the Tory MP, Bob Stewart, was also amended to show it had been tabled by another Tory MP, Oliver Colvile, after Stewart denied making it. It is understood both Beith and Stewart complained to parliament officials. In a letter to Heywood, Prescott writes: "I am concerned about a number of procedures involving these PQs which are being investigated by the Vote Office." Prescott has also questioned how the Department for Communities and Local Government chose to publish its procurement card spending figures.

According to government guidelines, information relating to procurement cards should be confined only to amounts above £500 and date back no further than 2008. However, in response to parliamentary questions, the department opted to publish figures revealing expenditure below £500, dating back to 2005. In his letter to Heywood, Prescott alleges "these written answers are nothing but part of a political campaign being carried out by Grant Shapps against me as I am now the Labour candidate for police and crime commissioner".

A Cabinet Office spokesman said that an administrative error was to blame for Prescott receiving two versions of the letter.

Local government minister Grant Shapps denied there was an agenda against Prescott. "He clearly hates transparency. If he wants to stand for public office, he should be held accountable for his actions."Prescott said: "We need to know as a matter of urgency who at the DCLG [department] demanded the changes to Lord O' Donnell's letter. Altering the most powerful civil servant in the land's correspondence without his permission is a very, very serious offence."

Last year O'Donnell became so alarmed at off-the-record briefings from government advisers he wrote to David Cameron urging him to restrain them.