Flight-Lieutenant Malcolm Kendall-Smith is to be court-martialled for “refusing to obey a lawful command” after he told his commanding officer that he would not go to Basra.

He is the first British officer to face criminal charges for challenging the legality of war.

Kendall-Smith, 37, unit medical officer for RAF Kinloss in Morayshire, has been decorated for his role in support of military operations in Afghanistan and for two previous tours in support of the RAF in Iraq.

However, after studying the legal position, including the advice of Lord Goldsmith, the attorney-general, he decided this year that the war was unlawful and it would therefore be wrong for him to return.

Justin Hugheston-Roberts, his solicitor, said preliminary court martial proceedings were expected to begin this year. He said that Kendall-Smith did not object in principle to serving in any war, provided it was legal.

“This is the first case of its kind involving Iraq. My client has considered this very carefully and in great depth. He is not arguing that he is a conscientious objector. He is arguing that the war is manifestly unlawful,” he said.

Kendall-Smith, as a serving officer, is barred by military regulations from talking to the media. A colleague said: “Malcolm joined the RAF out of a spirit of idealism. He felt he wanted to do something good, to make a difference. It was good old battle of Britain stuff, helping the good guys fight the fascists.

“When he first went to the Gulf in 2003, his awareness of the legal position was far less than it is now. He is now in no doubt that the war was illegal and that the government has spun its position on the evidence. He takes the view that this is something which is worth going to prison for.

“When he explained to his commanding officer that he thought the war was unlawful, he was told that the attorney-general had declared it legal. Malcolm simply replied that the attorney-general had said one thing, then later said more or less completely the opposite.”

A central part of Kendall-Smith’s legal case will be the manual of RAF law which states that a serving officer is justified in refusing to obey a command if it is illegal. His lawyers will also argue that his commission, granted by the Queen, requires him to act according to “the rules and discipline of war”.

International lawyers have argued that there was no legal justification for invading Iraq because Britain and America failed to wait for the United Nations to pass a second resolution specifically sanctioning military force.

Kendall-Smith was born in Australia but brought up in New Zealand where he studied to become a doctor. He has dual British-New Zealand citizenship and was commissioned as an officer in 2000. He earns about £40,000 a year.

He is posted with a staff of four at the regional medical centre at Kinloss, which employs more than 3,000 military personnel and is home to the Nimrod Maritime Reconnaissance Aircraft fleet.

He was suspended on full pay after being interviewed by the Royal Military Police in June. On October 5 he was charged after being served with court martial papers by the RAF prosecuting authority in Innsworth, Gloucestershire.

The Ministry of Defence said: “An RAF officer is due to appear before a general court martial on a date and location yet to be confirmed. The officer will be charged with four counts of disobeying a lawful command. It would be inappropriate to give further details.”

Hugheston-Roberts said: “We will be seeking a judge’s ruling on a huge volume of jurisprudence as to the legality of the armed conflict.”

The court martial will be heard at a military base by a senior judge and a board of at least five high-ranking officers, with an air commodore as president. There will be no jury and the case will be heard on a military base. The RAF will pay his defence costs but the reserves the right to reclaim the money if he is convicted.

Two years ago Leading Aircraftsman Mohisin Khan, a Muslim reservist from Ipswich, was disciplined after he refused to serve in Iraq because of his religious beliefs.