The vetting panel for the House of Lords warned Downing Street against awarding a peerage to Michael Martin, the former Commons Speaker, The Times has learnt.

The House of Lords Appointments Commission suggested that elevating Mr Martin, the first Speaker to be ousted in 300 years, would damage the reputation of the second chamber.

Its misgivings were overruled by Gordon Brown, who played a key role in telling Mr Martin that he had lost the confidence of the Commons but ensured that he would follow his predecessors to the Lords.

MPs have been informed that the Queen has sent a message to Parliament that she wishes to confer on Mr Martin “some signal mark of her royal favour” — taken to mean a peerage. This follows a Commons motion passed on Monday last week, urging the Queen to honour Mr Martin “for his eminent services during the important period in which he presided with such distinguished ability and dignity in the Chair of this House”.

The Times understands that before that decision was taken the commission — knowing that Speakers traditionally become peers on retirement — discussed whether the honour would be appropriate in Mr Martin’s case. His handling of the expenses row led Mr Martin to become the first Speaker to be forced out of office since 1695. It became clear that he had lost the support of the House, including the Government and Mr Brown, an old friend.

Mr Martin was also mired in controversy last year over the police raid on the office of Damian Green, the Shadow Immigration Minister. A private conversation between Mr Brown and Mr Martin was believed to have been critical in his decision to stand down.

The Times understands that the commission, chaired by Lord Jay of Ewelme, former Permanent Secretary at the Foreign and Commonwealth Office, raised doubts as to whether Mr Martin’s elevation to the peerage would harm the standing of the Upper House. MPs would not have been aware of the warning when they made their decision.

It is highly unusual for the commission’s advice to emerge in public, suggesting a degree of anger in the Lords over Mr Martin’s imminent arrival.

The commission has no power of veto and raised its doubts in a private submission to Downing Street. A source said that it was the commission’s duty to raise issues that it felt to be relevant even though in the case of a former Speaker, the honour of a peerage was virtually unanimously granted. The commission did not advise Mr Brown not to recommend Mr Martin for a peerage; it merely raised questions that it felt he should take into account.

Downing Street said yesterday that the decision to grant Mr Martin an honour was on the basis of a recommendation from the House of Commons in an uncontested motion. Labour MPs said that it would have been vindictive to have denied him a peerage, given his decision to resign to enable the Commons to make a clean break after the expenses scandal.

His supporters said that he was forced out because he was “Scottish, working-class and Catholic”.

Lord Lawson of Blaby, a Tory former Chancellor, said that a peerage for Mr Martin was a “mistake and unfortunate”.

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