Yesterday’s session at the Royal Courts of Justice was taken by surprise just before it ended, when James Dingemans, QC, counsel for the inquiry, revealed an e-mail from Mr Gilligan sent to a member of the foreign affairs committee suggesting questions to put to Dr Kelly.

At the point that the e-mail was sent, Dr Kelly had already come forward to admit to having talked to Mr Gilligan, but the BBC had refused to reveal its source.

However the e-mail from Mr Gilligan to a researcher working for David Chidgey, the Liberal Democrat MP on the committee, not only suggested pertinent questions for Dr Kelly to answer but also appeared to offer serious clues that Dr Kelly was indeed the BBC’s source.

The BBC’s difficulties will be increased because Mr Dingemans made a point of telling the inquiry that the corporation had not offered up the e-mail in question and that it had come to the inquiry from a different source.

Sources at the BBC were reported to be astounded by the revelation to the inquiry and there were signs that the corporation was again divided over the affair. Martha Kearney, political editor of Newsnight, said on last night’s programme that the e-mail implied that Mr Gilligan was revealing Dr Kelly as the source of a report by Susan Watts, the programme’s science editor, at a time when the BBC was protecting his identity.

After referring to two previous stories on weapons of mass destruction that quoted Dr Kelly as a source, Mr Gilligan said: “He also told my colleague Susan Watts, science editor of Newsnight (who described him as a ‘senior official intimately involved with the process of pulling together the . . .’ ”

The e-mail then ran to a second page that was not referred to in yesterday’s hearing and was therefore not released with the other evidence published by the inquiry. However, this was the form of words used by Ms Watts to describe the source for her report about the Iraq dossier.

Officials working for the inquiry told The Times last night that they were unable to provide a copy of the second page as a result.

In his e-mail to Mr Chidgey, Mr Gilligan went to great lengths to emphasise Dr Kelly’s seniority and expertise, pointing out that he had been described as the MoD’s senior adviser on biological warfare, the West’s leading biological warfare inspector and a world expert in the field.

The e-mail was sent by Mr Gilligan to Greg Simpson, the Liberal Democrat’s deputy head of press, to pass on to Mr Chidgey. A Liberal Democrat official said that the BBC journalist knew Mr Simpson, but was unable to say which man initiated the approach.

Mr Chidgey said in a statement: “I passed this e-mail on to the Hutton inquiry in case it had some relevance to their line of questioning. The e-mail was sent to me by Andrew Gilligan via one of our press officers. We must remember that at the time the (committee was)unaware that Dr Kelly was Andrew Gilligan’s source.”

The e-mail was disclosed by Mr Dingemans while Alastair Campbell was giving evidence. Mr Dingemans said that it looked as if Mr Gilligan was using the committee to “get at the Government”.

Helen Liddle, a former Scottish Secretary, said on Newsnight last night that it would have to be considered whether Mr Chidgey’s questions to Dr Kelly made the weapons expert realise that his cover had been blown.

She said: “It may well be that Andrew Gilligan has revealed Susan Watts’s source without involving Susan Watts in that process.

“We also have to take into account the pressure that may have been put on Dr Kelly as a consequence of him perceiving from the questions of Mr Chidgey that his cover had been blown, in effect.

“This has created a very serious situation for the BBC. We have a situation with the BBC where a correspondent has crossed the line from being an observer to being a participant in giving questions to an MP on a select committee.”

Menzies Campbell, the Liberal Democrats’ foreign affairs spokesman, said that Mr Chidgey had behaved properly and that the e-mail raised serious questions for Mr Gilligan.

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