The head of the NHS has laid bare his fears that the government's controversial reforms of the health service could end in "misery and failure".

Sir David Nicholson, chief executive of the NHS, said high-profile, politically driven changes almost always end in disaster. He warned against "carpet bombing" the NHS with competition but said that competition was best used like a "rifle shot" to fix problems.

The outspoken comments, made to GPs at a conference held by the Royal College of General Practitioners, puts Nicholson on a collision course with the new health secretary, Jeremy Hunt. Last week Hunt told the Conservative party conference that the NHS reforms devised by Andrew Lansley to open up the NHS to private providers and give extra powers to GPs were "brave and right". But Nicholson, who has until now kept his concerns private, revealed tensions between the government and the highest echelons of the NHS at the meeting held just over a week ago.

Nicholson said that he believed the reforms could serve patients well by offering them choice, and testing current failing services with competition. But the Observer has learned that he also voiced his worries about the potential burden of extra responsibilities given to GPs, including negotiating with private health providers. He said: "If we are creating a system where general practitioners feel it is their job to do all that, then I think we have a massive problem. We need to create the right kind of people with the right kind of skills, which we are trying to do at the moment through commissioning support, to enable people to focus their attention on clinical decision-making.

"My advice to anyone – and I have been involved in the last five or six years with the national programme for IT, and I have, as they say, the scars on the back around all of that – is that big, high-profile, politically driven objectives and changes like this almost always end in misery and failure."

Lansley was removed from the Department of Health in the last reshuffle but the government continues to pursue its £3bn shakeup of the NHS. This month 6,000 NHS services are up for tender to the private and third sector – such as voluntary and community services – including diabetes education, glaucoma treatment, abortion clinics and minor oral surgery.

Nicholson told GPs that he believed competition could be healthy, but reiterated a warning issued by the chair of the health select committee, Stephen Dorrell. Nicholson told the meeting: "It is very effective when it is used as a rifle shot to deal with specific issues rather than a carpet bombing."

Nicholson added that he believed the reforms were an opportunity to keep the politicians out of the NHS. He added: "I'm an optimist by nature, I have been a health service manager for the last 35 years." But in regard to the reform programme, he added: "What it does do is change the nature of the relationship between government and the NHS in a really profound way. We can conspire to stop it if we want to. We now have an NHS commissioning board, clinical commissioning groups, whose responsibilities are in law, statutory bodies with a legal framework. No longer is the NHS what the secretary of state said it would be. It creates much more difficulty for politicians to arbitrarily get involved in the day-to-day operations of the NHS."

A source close to Nicholson said the NHS chief had been attempting to rally GPs involved in the reforms to work with the changes.

Shadow health secretary Andy Burnham seized on Nicholson's comments. He said: "David Nicholson is a man who has the NHS at heart, so it is worrying to hear him talk in these terms. He has put on a brave face in public, but clearly has private concerns about the real damage this reorganisation is doing.

"His open acknowledgment of the possibility of it ending in failure will send shock waves through the NHS and provide a stark illustration of the sheer scale of the gamble the government is taking."

A Department of Health spokesperson said: "David Nicholson was speaking in favour of increased autonomy of our NHS and about strong local leadership of healthcare, which is something the government supports."