An RAF doctor who refused to serve in Iraq because he thought that the war was illegal will be court-martialled, a judge ruled today.

Flight Lieutenant Dr Malcolm Kendall-Smith faces two years in prison if he is found guilty of five counts of disobeying lawful orders.

Dr Kendall-Smith, 37, had served in Afghanistan and already completed two tours of duty in Iraq when he refused to return to the country last year.

Philip Sapsford, QC, defending, had argued his client believed he had a moral obligation to object to orders which he thought were illegal.

"The flight lieutenant’s case is that Iraq was and remains under occupation," Mr Sapsford said at a pretrial hearing last week. "He is entitled to say to this tribunal ’I hold that belief honestly and in these circumstances it’s my duty to disobey these orders’."

But Judge Advocate Jack Bayliss flatly rejected the argument today, even telling Dr Kendall-Smith, the first British officer to be tried for disobeying orders in the war, that he had an inflated sense of his role in the conflict.

Mr Bayliss said that by the time Dr Kendall-Smith was being ordered back to Basra for the third time, in the summer of 2005, the British military presence in Iraq had been legally assured by both the Iraqi Government and the UN for more than two years.

"None of the orders given to the defendant in this case was an order to do something which was unlawful," he said.

"There is no ambiguity in the wording of either Resolution 1511 or Resolution 1546," said Mr Bayliss, referring to the two UN resolutions passed after the invasion of Iraq by the US-led coalition in March 2003.

"It follows that I regard those resolutions as clear authority by the United Nations Security Council for the presence of British forces between the limiting dates in the charges faced by the defendant, namely June 1, 2005, and July 12, 2005."

Mr Bayliss's decision to concentrate on the status of the war in 2005, rather than the disputed circumstances of the original invasion, obviated the basis of Dr Kendall-Smith's case.

The doctor, a unit medical officer for RAF Kinloss in Morayshire who has joint British and New Zealand citizenship, was decorated for his service in Afghanistan.

But he claimed that after studying legal arguments about the war in Iraq, including the advice of the Attorney-General, Lord Goldsmith, he had come to believe that the British presence in the country was illegal.

But Mr Bayliss said that even if the Government had committed an act of illegal aggression in invading Iraq, Dr Kendall-Smith was wrong to imagine that he had any responsibility for it. "If a defendant believed that to go to Basra would make him complicit in the crime of aggression, his understanding of the law was wrong," he said.

Mr Bayliss said Dr Kendall-Smith's junior rank absolved him of responsibility, a subject he returned to when he addressed Mr Sapsford's argument that Dr Kendall-Smith had conceived himself as a leader rather a foot soldier in the war.

"If that was the defendant’s belief it was based on a greatly inflated sense of his own position," said Mr Bayliss. "Whatever may have been the defendant’s belief as to his status, it is disingenuous to argue that he was a leader. He was a non-combatant of relatively junior rank and cannot possibly have been in any way responsible for policy."

Dr Kendall-Smith's court martial will begin in Aldershot on April 11. According to the Ministry of Defence, he faces imprisonment for up to two years, dismissal from the armed forces, demotion or a reprimand.

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