A SECRET Whitehall unit has been working for weeks with the Pentagon on the overthrow of President Saddam Hussein and his replacement by a military administration that would run Iraq, much as allied governments did in Germany and Japan after the Second World War.

According to British and American officials, the final touches are being made to the ambitious plan, which envisages deploying an entire civil administration to take over the running of Iraq, from healthcare to education and security.

The Times has learnt that most of the key posts in the future Iraqi civil service will be held by former American generals, diplomats and aid workers, who will report directly to the Pentagon.

The overall head of this de facto Iraqi government will be General Tommy Franks, the commander-in-chief of American and British forces that are now poised to invade the country. Until yesterday Britain’s role in planning for post-Saddam Iraq was kept secret, even though the special inter-ministerial Iraq Planning Unit was created two months ago. It is headed by Dominick Chilcott, a Foreign Office diplomat and former Royal Navy officer, who co-ordinates with officials from the Ministry of Defence and the Department for International Development.

A Foreign Office official said that the existence of the unit was not revealed because they did “not want to give the impression that war was inevitable”.

British and American officials said yesterday that allied forces were bound by international law to take responsibility for running Iraq once the Baathist regime of President Saddam is overthrown. They insisted, however, that they would gladly hand over responsibility for civilian administration to the United Nations and ultimately to an elected Iraqi government once the situation had stabilised.

US officials denied that there was any intention of installing a long-term military “maharajah” and envisage a brief, “necessary occupation” lasting “months”.

Some Iraqis, probably drawn from exiled groups and figures inside the country, will initially be involved on a consultative basis. Later it is hoped that power will be transferred to an Iraqi Interim Authority.

Nevertheless, it is clear that General Franks will become a modern version of General Douglas MacArthur, who defeated and later ran Japan after the Second World War.

The civilian administrator will be General Jay Garner, a retired army officer who headed the rescue operation for Iraqi Kurds at the end of the last Gulf War.

He was put in charge of the Pentagon’s Office of Reconstruction and Humanitarian Assistance for Iraq in January, which will form the core of the new administration. General Garner’s staff of about 200 people is expected to deploy to Iraq the moment security is established. Many of his subordinates have already been sent to the region.

British officials have been seconded to the team. Some are working at his office in the Pentagon. Others are in Kuwait ready to move into Iraq.

Both the British and American officials said that they wanted to involve the UN as soon as possible, in spite of the divisions that emerged this week over the looming war.

But no one can predict how long it will take to defeat the Iraqi regime, restore order, guarantee security and lay the foundations for a future democratic state. There are fears that the longer the allies control the country the harder it will be to withdraw.

There is already anger and suspicion about US motives, after it was revealed that multibillion-pound contracts for reconstruction in Iraq have so far only been offered to American companies.

International aid organisations complained yesterday that their independence would be damaged if they were forced to work under US military authority.

Certainly the Pentagon planners are leaving nothing to chance and have already assigned key posts in the future civil service, including regional administrators, who would effectively control the old Ottoman empire governates of Mosul, Baghdad and Basra.

They will each have a core staff of about 12 who will work with the approximately 100 “free Iraqis” who are being recruited as advisers to the interim authority as it reshapes the Government.

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