A Foreign Office official involved in drafting the discredited dossier on Iraq's weapons of mass destruction suggested that he might have to review an assessment of Saddam's nuclear capabilities so that it was in line with briefings from Labour spin doctors, an internal Whitehall memo shows.

The March 2002 memo, written by Tim Dowse, head of the Foreign Office non-proliferation department, and sent to a special adviser to the then foreign secretary, Jack Straw, has been obtained by the Observer under the Freedom of Information Act.

In the memo, Dowse complains his department had been given "no forewarning" of a paper the special adviser used to brief the Parliamentary Labour Party and later the cabinet, which effectively contradicted the official assessment of Iraq's nuclear capability.

Dowse's memo, which was copied to officials including Sir Michael (now Lord) Jay, then the top civil servant at the Foreign Office, complains that while the briefing claimed that "if Iraq's weapons programmes remain unchecked, Iraq could … develop a crude nuclear device in about five years", the government's official line was that "the Iraqi nuclear programme is not 'unchecked' ". This was an acknowledgement that sanctions against Saddam's regime had constrained his nuclear ambitions.

The briefing found its way into the press with newspapers claiming that "Saddam could develop a nuclear weapon within five years".

Dowse notes that the official line on Saddam's nuclear capability is used "in the draft public dossier on 'WMD programmes of concern' which the Cabinet Office are producing at No 10's request". He adds: "We clearly will now have to review that text, to avoid exposing differences with your paper."

That dossier was the controversial document alleged to have been "sexed up" under the influence of spin doctors.

Dr Brian Jones, the former head of the WMD section at the Defence Intelligence Staff, told the Observer: "At first glance the Dowse memo appears to be a shot across the bows of the political wing of the Foreign Office. However, looking closer, it suggests a willingness of officials to bend intelligence assessments to fit the political requirement."

In the Observer in July, Carne Ross, the UK's Iraq expert at the United Nations from 1997 to 2002, said the Foreign Office tried to dissuade him from referring to the memo in his written evidence to the Chilcot inquiry. Ross said: "It's safe to assume that they realised that this document is a clearly smoking gun, illustrating how the public exaggeration of the WMD threat proceeded."

A Foreign Office spokesman said: "We are not going to comment on what witnesses might say, why the inquiry has called them, or what their lines of investigation should be."