The Archbishop cancelled his visit on Tuesday, complaining that the government was trying to restrict his movements. Although the trip was planned well in advance, on 21 December the government insisted that he come as its guest. He accepted the invitation but did not want his programme changed as a result.
Yesterday Dr Carey flew to Nimule, which in a rebel-controlled area where there are thousands of refugees from the civil war, as well as from the war between the two wings of the Sudan People's Liberation Army (SPLA).
The flights are illegal. The pilots of the small chartered aircraft based in Nairobi file false flight plans, giving Kenyan or Ugandan 'destinations' when they fly into southern Sudan.
Dr Carey's visit to the south will be fraught with political sensitivities as he tries to remain impartial between the bitterly divided factions of the SPLA. One wing is led by John Garang, who has led the SPLA since the war began 10 years ago, and the other by Riek Machar, his former deputy.
They have been divided along tribal lines but are also split over the basic aims of the movement. One of Dr Carey's tasks will be to try to prevent the churches splitting along similar lines to the SPLA. It is understood that he hopes to meet both leaders but has chosen to visit two towns, Akot and Yambio, which are controlled by Mr Garang's faction and is not planning to visit Mr Machar's area.
Although much of the suffering Dr Carey will witness will have been caused by the war between these two men and their followers, he will also taste the strong resentment of the Christian southerners against the northern Islamic government. Recent visitors to the south have been greeted by flags bearing the cross of St George - not a quaint way of welcoming an Englishman but an expression of crusading fervour against forced Islamicisation and the repression of Christians.
As far as Khartoum is concerned, cancellation of the Archbishop's visit to the capital will confirm all the northerner's deepest prejudices about Britain and British Christianity. Many believe Britain tried repeatedly to split southern Sudan from the north when Sudan was part of the Anglo-Egyptian condominium and that it has supported rebel and secessionist movements in the south ever since. Suspicion of Britain goes back to the days of General Gordon and the battle of Omdurman 100 years ago, and the struggle between Christianity and Islam to control the Nile.
Although the Khartoum government, which came to power in a coup in 1989, is strongly Islamic, it is anxious to maintain whatever contact it can with the rest of the world, and fears becoming isolated. The expulsion of the British ambassador indicates that it takes the cancellation of the visit so seriously that it is prepared to allow already strained relations to be broken.
In February the Pope visited Khartoum as a guest of the government, but preached strongly against religious intolerance. Relations between the government and the Vatican however, have improved steadily and a Sudan ambassador has been appointed to the Vatican.