Government and press often have a love-hate relationship, but a tiff turned into a sustained clash last week after the disclosure by the New York Times of a secret US government effort to monitor international money transfers.

The tracking programme isn't new, and its legality is not seriously in question, but with the fifth anniversary of the 11 September attacks approaching and the administration's holiday from press scrutiny long over, it has become the touchstone for the most hotly debated subject in American life: the conduct of the 'war on terror'.

The data-tracking operation is only the latest clandestine programme the US press has exposed this year. It comes on the heels of a Washington Post report on secret CIA prisons abroad and an NYT scoop in January that revealed President Bush had authorised the National Security Agency to eavesdrop on American citizens without court warrants.

Though the new report does not have the import of either of the previous exposés, the NYT's decision to publish it over the sustained objections of the administration has given White House strategist Karl Rove - now free of his legal worries - a rare opportunity to rally the support base.

In Republican America, in need of uplift after recent failures to pass anti-gay marriage legislation or enact a permanent repeal of death duties, accusing the paper of undermining the war on terror is an easy hit. The New York Times, after all, is shorthand for every bogey at Republican spin-masters' disposal: it means liberal, gay, Jewish, intellectual, big-government, pro-choice, unpatriotic.

For the paper's constituency, too, the existence of a programme to monitor money transfers re-confirms fears that Bush's regard for authority echoes Nixon's Vietnam-era assertion that the executive branch of government has the 'inherent authority' to spy on anyone it deems to be the enemy.

The fact that the US government is trying to glean information from the vast database of financial transactions maintained by Swift, the Belgium-based payments and clearing consortium, is not a surprise. Tracking bank transactions as a means of pursuing potential terrorists has been central to US intelligence efforts since before 9/11, and its importance has been reiterated several times since 24 September 2001, when Bush asserted: 'We're putting banks and financial institutions around the world on notice: we will work with their governments and ask them to freeze or block terrorist ability to access funds in foreign accounts.'

None the less, in choosing to reveal the specifics of the monitoring effort - known as the Terrorist Finance Tracking Program - the NYT has come in for sustained criticism. Bush called the paper's conduct 'disgraceful' and told a fundraiser in St Louis last week: 'This programme has been a vital tool in the war on terror. There can be no excuse for anyone entrusted with vital intelligence to leak it - and no excuse for any newspaper to print it.'

Vice-President Dick Cheney said the paper had made it 'more difficult for us to prevent attacks in the future'. The National Review, a conservative weekly magazine, suggested the NYT should be stripped of its White House press credentials.

In Congress, a resolution was drafted supporting the data-tracking programme and condemning the publication of its existence. The resolution said it 'expects the co-operation of all news media organisations in protecting the lives of Americans and the capability of the government to identify, disrupt and capture terrorists by not disclosing classified intelligence programmes'.

Further, the director of national intelligence and US ambassador to the United Nations in the run-up to the invasion of Iraq, John Negroponte, ordered a review of any damage to counter-terrorism efforts resulting from the leak. The right-wing Weekly Standard called the NYT a 'national security threat... drunk on its own power'. New York Republican congressman Pete King said the paper had an 'arrogant, elitist, left-wing agenda' and should be prosecuted.

There is surprise at quite this level of fury being directed at the paper. 'Even by modern standards of media-bashing, the volume of vitriol... is remarkable,' notes Washington Post media critic Howard Kurtz - especially given that the Los Angeles Times, the Washington Post and the Wall Street Journal also published accounts of the programme.

The NYT's executive editor, Bill Keller, suggests the paper's critics are still angry at it for disclosing the government's domestic eavesdropping programme. 'In their view, this adds insult to injury... The Bush administration's reaction roused their base, but also roused the anti-Bush base as well,' he says.

But besides political expediency, there are deeper reasons for the government's protest. The paper's actions threatens what is known as the 'New Paradigm' - a reading of the US constitution that rests on the idea that the President, as commander-in-chief, has authority to override legal restrictions in the name of national security. This reading, which took a fresh blow on Thursday when the Supreme Court struck down the legality of holding military tribunals for prisoners in Guantanamo, remains the centrepiece of the administration's wartime thinking.

The Bush White House likes to appear blase about the media, but it makes strenuous efforts to get the right message out. In an address to the Council on Foreign Relations in February, Secretary of Defence Donald Rumsfeld told its members that the US was losing the war of ideas. Now, he added, 'some of the most critical battles may not be in the mountains of Afghanistan or the streets of Iraq, but in newsrooms - in places like New York, London, Cairo, and elsewhere'.

To win the war of influence, Rumsfeld's Pentagon established several well known but clandestine-sounding programmes, including the 'Office of Strategic Influence' and the 'Office of Global Communications', which operated with a view to 'developing, co-ordinating, de-conflicting and monitoring the delivery of timely, relevant, and effective messages to targeted international audiences.'

But according to 'Mind Games,' a study of the government's strategy to frame reality published by the Columbia Journalism Review, the true purpose of the OSI and the Office of Global Communications was not to shape international opinion.

'The global issue wasn't the reason why they were created,' Daniel Kuehl, a retired Air Force colonel at the National Defence University, told the magazine. 'They clearly had a completely domestic focus. They were part of the effort to re-elect the president... their goal was psychological operations on the American voting public.'

In 2002, the New York Times exposed the existence of the OSI and it was disbanded shortly thereafter, its duties assigned elsewhere. The Office of Global Communications also now seems to be inactive. But the Pentagon's desire to use the media as a weapon has not ended. Instead, the line between providing information and spreading propaganda has further blurred.

The 'war on terror' (now being called 'the long war') is increasingly viewed as one of values and ideologies. With the NYT's editorial opposition to the war established, it is an obvious target. It was never a soldier to the Republican cause (although it was at least unwittingly complicit in supporting plans for the war by offering enthusiastic, but incorrect, evidence of Saddam Hussein's alleged weapons of mass destruction).

Keller says he spent an hour with Treasury secretary John Snow listening to arguments for not publishing the money-transfers story.

'I always start with the premise that the question is, why should we not publish? Publishing information is our job,' he later explained. 'What you really need is a reason to withhold information.' And this, it seems, could not be found.