Scientists who drew up the key World Health Organisation guidelines advising governments to stockpile drugs in the event of a flu pandemic had previously been paid by drug companies which stood to profit, according to a report out today.

An investigation by the British Medical Journal and the Bureau of Investigative Journalism, the not-for-profit reporting unit, shows that WHO guidance issued in 2004 was authored by three scientists who had previously received payment for other work from Roche, which makes Tamiflu, and GlaxoSmithKline (GSK), manufacturer of Relenza.

City analysts say that pharmaceutical companies banked more than $7bn (£4.8bn) as governments stockpiled drugs. The issue of transparency has risen to the forefront of public health debate after dramatic predictions last year about a swine flu pandemic did not come true.

Some countries, notably Poland, declined to join the panic-buying of vaccines and antivirals triggered when the WHO declared the swine flu outbreak a pandemic a year ago this week. The UK, which warned that 65,000 could die as a result of the virus, spent an estimated £1bn stockpiling drugs and vaccines; officials are now attempting to unpick expensive drug contracts.

The cabinet office has launched an inquiry into the cost to the taxpayer of the panic-buying of drugs.

Today, the Council of Europe, produces a damning report into how a lack of openness around "decision making" has bedevilled planning for pandemics.

"The tentacles of drug company influence are in all levels in the decision-making process," said Paul Flynn, the Labour MP who sits on the council's health committee. "It must be right that the WHO is transparent because there has been distortion of priorities of public health services all over Europe, waste of huge sums of public money and provocation of unjustified fear."

Although the experts consulted made no secret of industry ties in other settings, declaring them in research papers and at universities, the WHO itself did not publicly disclose any of these in its seminal 2004 guidance. In its note, the WHO advised: "Countries that are considering the use of antivirals as part of their pandemic response will need to stockpile in advance."

Many nations would adopt this guidance, including Britain. In 2005, the government said it had begun bulk-buying the drug Tamiflu, initially ordering 14.6m doses after bird flu killed 40 in Asia.

The specific guidance on antivirals was written by Professor Fred Hayden. He has confirmed in an email that he was being paid by Roche for lectures and consultancy work at the time the guidance was produced and published. He received payments from GSK for consultancy and lecturing until 2002. He said "[declaration of interest] forms were filled out for the 2002 consultation".

The previous year Hayden was also one of the main authors of a Roche-sponsored study that asserted what was to become a main Tamiflu selling point – its claim of a 60% reduction in flu hospitalisations.

Dr Arnold Monto was the author of the WHO annex dealing with vaccine usage in pandemics. Between 2000 and 2004, and at the time of writing the annex, Monto had openly declared consultancy fees and research support from Roche and GSK. No conflict of interest statement was included in the annex published by the WHO.

When asked if he had signed a declaration of interest form for WHO, Dr Monto said "conflict of interest forms are requested before participation in any WHO meeting".

The third scientist, Professor Karl Nicholson, is credited with the WHO's influential work Pandemic Influenza. According to declarations he made in the BMJ and Lancet in 2003, he had received sponsorship from GSK and Roche.

Even though the previous year these declarations had been openly made, no conflict of interest statement was included in the annex. Nicholson said he last had "financial relations" with Roche in 2001.

When asked if he had signed a declaration of interest form for WHO, he replied: "The WHO does require attendees of meetings, such as those held in 2002 and 2004, to complete declarations of interest."

A WHO official told the BMJ it had to balance an individual's privacy with the robustness of guidelines, which were subject to a wide external review process.