Documents obtained by the Guardian under Freedom of Information legislation reveal that:

- The world's biggest drug company, Pfizer, warned ministers that it could take its business elsewhere. "Pfizer ... noted that there is complacency in some quarters of Whitehall regarding their continued investment in the UK," the minutes of the meeting record.

Ministers later agreed to a special meeting where six companies could lobby for their drugs for Alzheimer's disease.

- Two companies lobbied ministers for wider access by patients to their drugs, both of which were later turned down by Nice on the grounds that they were not effective enough and too expensive.

The pharmaceutical industry is a major contributor to the UK economy. Its total investment in research and development was more than £3.4bn in 2004, which, a Whitehall briefing note points out, "represents around a quarter of the UK's total manufacturing industry expenditure".

Decisions by Nice, set up seven years ago, are crucial for the companies. It decides whether a drug should be universally available to patients in the NHS. Chaired by Prof Sir Michael Rawlings, Nice draws on scientific experts and consults doctors, patients, drug companies and the Department of Health. The government invariably accepts its final recommendations. Although ministers say they cannot influence Nice, the documents reveal a constant stream of high-level visitors from drug companies.

Manufacturers, led by Pfizer, have been complaining to ministers about Nice's position on their controversial Alzheimer's drugs. Originally Nice decided to allow them, then it reversed its position, saying they should be used only for a minority of patients with moderate disease.

At a meeting in October with the minister, Pfizer executives made it clear they "were unhappy with the Nice decision ... and thought their processes were flawed". They requested a special meeting with ministers where all the companies making Alzheimer's drugs could put their case.

The documents prepared by civil servants for the Pfizer meeting outline the wealth and scale of the US company, which in 2004 had revenue of $52.5bn (£28bn) and a net income of over $11bn.

But, Pfizer executives warn the minister, it could always take its business elsewhere. "Pfizer ... noted that there is complacency in some quarters of Whitehall regarding their continued investment in the UK," the minutes record. "Pfizer asked for more public support from the government for a robust pharmaceutical industry in the UK and more consultation/dialogue with the government."

The subsequent meeting with all the companies took place in December. The minister, Jane Kennedy, was confronted by eight managing directors, vice-presidents and senior executives from six drug companies. The executives lobbied hard for the Nice ruling to be overturned by the government.

A memo reports the summing-up of Johnson & Johnson's vice-president David Brickwood: "Nice should take into account what the companies see as the overwhelming views of patients, carers and clinicians on the efficacy of the drugs."

In a statement, Pfizer said it "regularly meets with key stakeholders, including government ministers, to keep them up to date with issues relating to our business". A variety of topics were discussed, it said.

"Nice and health technology assessment remains a topical issue coupled with the proposed ban on medicines for mild Alzheimer's disease. We believe this is the wrong decision and have appealed along with other manufacturers of anti-dementia medicines."

In February, Eli Lilly lobbied hard for its drug Alimta, designed to treat the asbestos-linked cancer mesothelioma. Its executives gave a presentation to Ms Kennedy, incorporating newspaper cuttings claiming that cancer victims were dying for want of the drug. The minister agreed that there should be a high-level meeting between her ministry and the Department for Work and Pensions.

But in June, Nice said there was insufficient evidence to show that Alimta was better than other cheaper treatments, recommending that the NHS should not use it. A Lilly spokesman said it was legitimate for the company to make representations to the DoH but it was not seeking to undermine Nice. "We are fully engaged and committed to the Nice process," he said

Pressure was brought to bear on ministers by another company, Johnson & Johnson, over its bone cancer drug Velcade. A briefing for Ms Kennedy before a meeting with the company's executives in November says: "Johnson & Johnson have written to the Department of Health numerous times over the past 12 months about Velcade." The company wanted its drug fast-tracked for approval by Nice.

Velcade was one of the five drugs Nice was asked by ministers to handle through its new fast-track procedure. But Nice's appraisal committee has given a preliminary opinion that it is not suitable for use in the NHS.

A Johnson and Johnson spokesman said the company was not trying to "unduly influence" Nice but it was legitimate to seek to persuade ministers to speed up the appraisal of Velcade. The company did not want to comment on its lobbying over Alzheimer's drugs.

In May, the health minister Andy Burnham met Peter Dolan, then chief executive of Bristol-Myers Squibb and chairman of the Pharmaceutical Research and Manufacturers of America (PhRMA), the powerful industry body in the US, which has been highly critical of Nice.

Richard Marsh, director of external affairs at Bristol-Myers Squibb, who also attended the meeting, told the Guardian that his company had wanted to raise a number of issues, including Nice, with the minister.

"Companies have a legitimate interest in getting the best for their products and getting a positive appraisal by Nice. Where they have an opportunity to raise issues with ministers, they can do that ... It may be that Nice has genuinely got a blind spot about something and a legitimate point can be made to ministers. I don't think the Nice process is necessarily undermined. It is up to the minister what they do with that information." He added that companies wanted to invest in countries with a "favourable environment".