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The archbishop was arrested when he arrived at Nicosia airport to board an airliner for Athens after refusing to denounce the use of violence. Britain has accused him of "actively fostering terrorism".
Three other nationalists accused of supporting guerrilla and other violent activities were also arrested - Bishop Kyprianos of Kyrenia, Polycarpos Ionnides, and Papastavros Papa-Aganthelou - and deported to an unknown destination.
The arrests come against a background of increasing violence against the British and the failure of the latest talks on the island's future.
The Greek Cypriot guerrilla group, EOKA, the National Organisation for Cypriot Combatants, was set up last year with the aim of ending British rule on the island and supporting "enosis", or unification with Greece.
Archbishop Makarios has been a leading figure in Cyprus's campaign for "enosis" and the right of the Cypriot people to self-determination. He is also said to have supported the creation of EOKA.
Today's arrest of the archbishop appears to have been carefully planned. Elaborate precautions were taken to prevent anyone from entering Nicosia airport, except for airline passengers, and all phone lines were cut.
This evening all shops in Nicosia were shut as news of the archbishop's arrest spread. There were fears EOKA might use the opportunity to cause trouble.
The Governor of Cyprus, Sir John Harding, said he had taken the decision to deport the archbishop because he had become "a major obstacle" to a return to peaceful conditions.
He said the arcbishop's influence had to be removed from the island in the interest of promoting peace, order and good government.
Sir John has also issued an order banning all long-distance calls to Greece until further notice. All internal telegrams and telegrams to and from Greece are subject to censorship until further notice.
Last month two RAF servicemen were shot dead and another seriously wounded on the streets of Nicosia. They were unarmed and wearing civilian clothes.
The attack led to growing demands from British supporters for the archbishop's deportation unless he renounced violence.
When the Secretary for the Colonies, Alan Lennox-Boyd, left Cyprus on 1 March after failing to make any progress in the peace talks, there were a series of bomb explosions in Nicosia, thought to have been carried out by EOKA terrorists.
One of the main sticking points in the talks was the Archbishop's demand for an amnesty for four terrorists facing the dearth penalty for political offences involving death and murder.
Britain declared Cyprus a crown colony in 1925. The island had for many years been under Turkish control, although it had a majority Greek population.
Britain sees Cyprus as an important strategic military base and fears union with Greece would lead to a military withdrawal.
The archbishop and his allies were deported to the Seychelles. The following day riots broke out in Cyprus. The United States and Greece condemned the British Government's decision and there were even objections from the Opposition Labour Party.
Archbishop Makarios was allowed to return to Cyprus when he finally gave up hope of "enosis", or unification with Greece. He received a tumultuous welcome in 1959 as chief Greek-Cypriot Minister in the new Greek-Turkish provisional government.
Later that year he became president and in 1960 Cyprus became independent.
In 1974, he was briefly deposed in a coup by Greek Cypriots seeking unification with Greece. Fearing for the rights of the minority Turkish population, Turkey invaded northern Cyprus and expelled Greek residents.
The island was officially divided and the buffer zone between the two sectors is still patrolled by the United Nations.
The Turkish-occupied sector declared itself the Turkish Federated State of Cyprus in 1975. The name was changed to the Turkish Republic of Northern Cyprus in 1983. Both declarations were recognised only by Turkey.
When Archbishop Makarios died in 1977 the posts of archbishop and head of state were officially separated.
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