AN MI6 director has quit amid reports of divisions at the top of the service.

Mark Allen, who was in charge of the Middle East and Africa department, left abruptly in the summer. He is said to have found it difficult to accept John Scarlett as chief.

Allen’s departure will add to the controversy surrounding MI6, which has been dogged by rumours of rifts since Scarlett’s appointment in May to replace Sir Richard Dearlove.

Tony Blair’s rejection of MI6’s own candidates in favour of Scarlett brought accusations of cronyism from political opponents who said the prime minister had rewarded Scarlett for saving the government’s reputation at the Hutton inquiry.

Allen, 54, was not due to retire until next July. An Arabist who worked under diplomatic cover in Abu Dhabi and Cairo, he is said to have been highly regarded within the service but “pleased to be out”.

He was credited with helping to persuade the Libyans to abadnon development of weapons of mass destruction. As one of MI6’s four directors, Allen’s duties covered running spying operations in the Middle East, including Iraq.

There are signs of unease within MI6 at what some allege is political interference. Relations between Scarlett and Allen were said to have been strained over the government’s controversial Iraq dossier.

In his former role as chairman of Whitehall’s joint intelligence committee, Scarlett had to prepare the dossier. Some senior intelligence officers disowned the document, saying it gave the impression that MI6 was more certain than it actually was about Iraq’s banned weapons.

The issue is likely to be reignited when the final report of the CIA-backed Iraq Survey Group is published shortly. If, as expected, it shows that no banned weapons were found during the 15-month search it will prompt new calls for reforms of the way the government handles intelligence.

Allen was also said to have been uncomfortable with aspects of strategy on Iraq. “His politics are not new Labour,” a source said.

Allen, who learnt Arabic at Oxford, will join BP as an adviser next month. He will be working with Sir Jeremy Greenstock, Britain’s former special envoy to Iraq. BP wants to exploit opportunities in the Middle East — including Iraq, which has the world’s largest oil reserves after Saudi Arabia.

Allen was one of three people who applied for the job of chief at MI6.

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