Liam Fox has vowed to tackle the "leak culture" at the Ministry of Defence after criticism from David Cameron about several unauthorised disclosures.
Details leaked to the press in recent months include a private letter from the defence secretary to the PM warning about excessive budget cuts.
A document expressing concern about the recent defence review was also leaked.
Dr Fox told the BBC that he had rebuked officials, adding such leaks were "unprofessional" and "unfair".
Speaking on Thursday, Mr Cameron said the spate of leaks was "worrying" and the MoD seemed to have "a bit of a problem" with the issue.
He said it was "regrettable" that Dr Fox's letter to him - in which the defence secretary warned about "draconian" cuts to defence - should have ended up in the public domain, saying it had created "added pressure" during already heated negotiations over the defence budget.
Dr Fox has always denied any knowledge of the leak - which is the subject of an ongoing MoD investigation.
Just hours before the prime minister's appearance before the liaision committee of MPs, the Daily Telegraph said it had obtained an internal MoD analysis of the defence review raising concerns that the process had "badly damaged the confidence and morale of our personnel".
In a BBC interview, Dr Fox was asked whether the prime minister's remarks represented a rebuke for him and his department.
"If the prime minister thought he was rebuking the department then he was in the amateur stakes, let me tell you on that one, because I was rebuking them much more over the culture of leaks we seem to have inherited," he told Radio Four's Today programme.
Dr Fox said it was important ministers and officials were able to discuss difficult issues in the knowledge that their conversations would not be made public.
"It is very easy to get, in a very big department, to get one or two people who will pass things out. I think it is unprofessional and very unfair to their colleagues who are then unable to discuss things in a free way."
"I hope it is a culture we can hope to change over time".
Dr Fox also said he had had no involvement in a letter sent to The Times by senior military commanders in support of the shake-up of the armed forces, which will see the scrapping of the Ark Royal aircraft carrier and the Harrier jump jets.
"I did not encourage them to write the letter. They were very keen to put on the record, not least to the members of their own forces, that they had thought about the issues, about the implications for operations and capabilities and they had assessed what we had to do against real world risks.
"The point they were making very clearly was, having taken these decision, they were very clear and standing foursquare behind them."
No 10 sources have said they played no part in the letter's drafting which followed criticism of the review from some service personnel who suggested it was driven by the search for huge financial savings rather than future security needs and capabilities.