The government is threatening to block the disclosure of emails that reveal who removed key sections from a letter that exonerated Lord Prescott of false claims that he had used a government credit card for "cavalier" spending.

Despite a ruling from the information commissioner that the details be released this week, ministers may prevent the release of emails between the Cabinet Office and the Department for Communities and Local Government. Ministers are contemplating a defence under section 36 of the Freedom of Information Act that release of the emails may prejudice the "effective conduct of public affairs" or "collective cabinet responsibility".

The emails centre on unfounded claims by the Tory co-chairman Grant Shapps, who was then a housing minister, that the former deputy prime minister's "private office" had spent £2,000 on Whitehall credit cards, supposedly including a trip to an Australian casino. In fact the spending was entirely legitimate. The only untoward items were due to the government-issued credit card having been cloned.

The letter from the head of the civil service, Gus O'Donnell, clearing Prescott was altered, with a key paragraph – apologising to the Labour peer Prescott for not warning him that information was being released – removed.O'Donnell's signature was apparently forged. The warning procedure allows former ministers to prepare a response to allegations raised about them in parliament.

Without this notice, Tory MPs were able to put down parliamentary questions and ambush Prescott. It led to a spate of newspaper stories conveying the impression that Prescott had enjoyed hospitality at the taxpayers' expense when he was deputy prime minister. Shapps, now Tory chairman, claimed: "Prezza seems to have a cavalier attitude to the public purse."

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.

He and Hilary Benn, Labour's frontbench spokesman on local government, have issued a series of freedom of information requests that have seen both the Cabinet Office and the Department for Communities and Local Government stall over the release of the key emails. Prescott said: "It is absolutely staggering Grant Shapps's former department redacted a cabinet secretary's letter without his permission and is now covering up whodunnit.

"This government is trying to protect the identity of the person responsible by using a ministerial veto clause to say it's not in the public interest. This from a government that claims a commitment to greater transparency. I know from the Cabinet Office that they have the answers as to who gave the order to change the cabinet secretary's letter. They must publish now."

The Cabinet Office said: "We believe that some of the information held is covered by section 36 and extra time is needed in order to make a determination whether the public interest is best served by releasing this information or not."

A spokesman for the communities department said: "We have not currently issued a section 36 exemption order. We will be writing to Lord Prescott in due course."

In answer to a parliamentary question on the matter, Lord Wallace, a government whip, told the Lords the missing paragraphs in the letter had been deleted in administrative error and that the cabinet secretary, Jeremy Heywood, had written to Prescott to "explain the background".

In a separate development it emerged on Sunday that the website founded by Shapps which Labour called for an investigation into last week over allegations of copyright violation and fraud has been taken down from the internet.