David Cameron has said a series of apparent government leaks about the defence review were "worrying".
The Daily Telegraph has published several documents including a letter from Liam Fox to Mr Cameron outlining concerns about excessive budget cuts.
Mr Cameron told a committee of MPs that leaks "don't help" and added to "public pressure" during budget talks.
But he said the review had resulted in a "good and sensible" outcome for the country's armed forces.
Mr Cameron was asked about the defence review just hours after a Ministry of Defence [MoD] document - leaked to the Daily Telegraph - suggested the way it was handled had "badly damaged" morale across the armed forces.
Up to 17,000 service personnel are set to lose their jobs under the proposals which ministers say will modernise the nation's military without compromising security.
The prime minister told the liaison committee of senior Commons backbenchers that the MoD did seem to have "had a bit of a problem" with leaks - adding that this was "worrying when it is the department responsible for security".
Asked specifically about Dr Fox's private letter - in which the defence secretary warned during the height of budget negotiations about "draconian" cuts to defence - he said it was to be expected that he should argue about the "importance of not making too deep cuts in defence".
"Ministers stand up for their departments and make the case for their departments," he said. Sometimes they do it orally, sometimes it appears in a letter. Regrettably, sometimes it appears in national newspapers."
Dr Fox has always denied any knowledge of the leak - which is the subject of an ongoing MoD investigation.
Mr Cameron said the row over the leak had not "materially changed" the outcome of the MoD's budget settlement - which will see its funding cut by 7.5% over four years.
But he added: "Leaked letters do not help. They add to public pressure... They mean meetings we are having are under intensive external scrutiny."
Mr Cameron confirmed there was a "gap" between what resources the MoD wanted and the savings the Treasury were seeking, adding that the defence budget inherited from Labour was a "bit of a train crash".
He said he had had to "interfere a bit" at the end of the process to "bring the two parties together to get a good and sensible outcome" - which he stressed would not affect operations in Afghanistan.
Published last month, the defence review promises the most far-reaching shake-up of the armed forces for decades.
Mr Cameron defended the decision to scrap the Ark Royal aircraft carrier and the Royal Navy's Harrier jump jet fleet, saying it might have been "easier" to keep them both but it would have been "wrong" for the UK's long-term needs.
He was also asked by MPs about a letter sent to the Times by military chiefs in support of the plans and whether No 10 had had any role in instigating it.
Mr Cameron said he did not know but he would not have been "at all surprised" if that was the case.
No 10 sources later said staff there played no part in the letter's drafting but the BBC's Political Correspondent Ross Hawkins said he had been told that Dr Fox suggested the letter to military chiefs after discussions with staff as a right of reply to earlier criticisms published in the Times.
Critics have said the review was driven by the search for huge savings rather than future security needs.
The Daily Telegraph reported on Thursday that an internal MoD analysis of the process raised concerns that the process had "badly damaged the confidence and morale of our personnel".
The speed at which the review, overseen by the National Security Council, took place meant there was insufficient time to consult allies, to take on board external advice and to prepare serving personnel for the scale of the shake-up, it said.
Dr Fox said the document was "not authorised" and did not reflect the thinking of senior officials, ministers or the chiefs of the armed forces - who had supported the process throughout.
Labour said the leak demonstrated the entire process had been flawed.
"Decisions were stitched up in Whitehall to meet the government's spending plans, not our nation's security needs," said shadow defence secretary Jim Murphy.
Former First Sea Lord and ex-Labour minister Lord West said the document illustrated the fact that many serving personnel felt "very bruised" by the apparent lack of consultation.
"The feeling people were not told is very clear and that is a concern," he told the BBC's Daily Politics.
However, he said the document "did not necessarily" reflect the opinions of senior military commanders.