The full extent of government anxiety about the state of British-Israel relations can be exposed for the first time today in a secret document seen by the Guardian.

The document reveals how the Foreign and Commonwealth Office (FCO) successfully fought to keep secret any mention of Israel contained on the first draft of the controversial, now discredited Iraq weapons dossier. At the heart of it was nervousness at the top of government about any mention of Israel’s nuclear arsenal in an official paper accusing Iraq of flouting the UN’s authority on weapons of mass destruction.

The dossier was made public this week, but the FCO succeeded before a tribunal in having the handwritten mention of Israel kept secret.

The FCO never argued that the information would damage national security. The Guardian has seen the full text and a witness statement from a senior FCO official, who argued behind closed doors that any public mention of the candid reference would seriously damage UK/Israeli relations. In the statement, he reveals that in the past five years there have been 10 substantial incidents and 20 more minor ones relating to Israeli concerns about attitudes to their government within Whitehall.

The Information Tribunal, which adjudicates on disputes involving the Freedom of Information Act, agreed to remove the single reference to Israel when it ordered the release of the draft of the Iraqi weapons dossier written by John Williams, the FCO’s chief information officer at the time.

Along with unfavourable references to the US and Japan, the reference to Israel was written in the margin by someone commenting on the opening paragraph of the Williams draft. It was written against the claim that “no other country [apart from Iraq] has flouted the United Nations’ authority so brazenly in pursuit of weapons of mass destruction”.

In statement to the tribunal, Neil Wigan, head of the FCO’s Arab, Israel and North Africa Group, said he did not know who had referred to Israel in the margin. He went on: “I interpret this note to indicate that the person who wrote it believes that Israel has flouted the United Nations’ authority in a manner similar to that of the Iraqi regime of Saddam Hussein.”

Its disclosure would seriously damage the UK’s relations with Israel, Wigan said. The comparison with Saddam and the “implied accusation of a breach of the UN’s authority by Israel are potentially very serious”. It was “inevitable” that relations between the UK and Israel would suffer if the marginal note were allowed to enter the public domain, he added.

Wigan observed: “Unfortunately, there is perception already in Israel that parts of the FCO [Foreign and Commonwealth Office] are prejudiced against the country”. The note on the Williams draft dossier “would therefore confirm this pre-existing suspicion and would increase the damage”.

Writing in October last year, he noted that “criticism of Israel received a huge amount of media coverage”. The margin comment mentioning Israel would thus be given a “high profile”. Harming relations with Israel would undermine the FCO’s ability to prevent and resolve conflict “through a strong international system”. In addition, there was “an important national interest in relation to counter-terrorism”, Wigan said.

The FCO insisted on the removal of the reference to Israel after it lost a long battle to suppress the draft dossier, which was drawn up in early September 2002. It originally argued that the name of the author needed to be protected. It then said the contents of the draft dossier should be suppressed to protect the need for officials to give frank advice. The Williams document was finally released by the FCO last week, three years after it was first requested by Chris Ames, an independent researcher, who pursued his campaign in the New Statesman magazine.

Richard Thomas, the Information Commissioner, said last year that it was in the public interest that the document should be released in its entirety. The FO appealed against his ruling and took it to the Information Tribunal.

The FCO had no objections to references to other countries in the margin of the Williams document. Alongside the claim that no other country apart from Iraq had twice launched wars of aggression against neighbours, the unknown FCO official writes: “Germany?” and ” US: Cuba, Guatemala, Mexico”. Against a reference to the use of chemical weapons, the official has written: “Japan in China?”

Claims in the Williams draft are similar to those in the final government Iraqi weapons dossier published in late September 2002. The Information Tribunal ordered the release of the draft, without reference to Israel, observing that it may have played a bigger role in influencing the final dossier than previously supposed. The government tried to distance itself from the Williams draft.