Silvio Berlusconi’s top ally in Italy’s coalition government has been accused of ordering an “extraordinary rendition” to help Kazakhstan’s dictator, President Nursultan Nazarbayev.

The wife and six-year-old daughter of leading Kazakh dissident Mukhtar Ablyazov were arrested and deported from Italy on 29 May on the orders of Rome’s interior ministry, which is headed by Angelino Alfano.

Mr Alfano, who also serves as Deputy Prime Minister, is a senior member of Mr Berlusconi’s conservative PDL party, and is seen as the former premier’s right-hand man in government.

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Mr Ablyazov’s wife was accused of holding a false passport and whisked out of Rome within 72 hours on a chartered jet, accompanied by a Kazakh official. But a Rome court has now ruled her documents were in order and it has questioned the validity and speed of the deportation.

Centre-left politicians and newspapers in Italy have accused Mr Alfano of delivering the wife and child of Mr Ablyazov to Kazakhstan at the behest of Mr Berlusconi, who has described the Kazakh President as “a dear friend”. Mr Alfano has, as justice minister under previous Berlusconi administrations, twice attempted to introduce immunity laws to shield the media mogul from prosecution – laws that were subsequently struck down as unconstitutional by the courts.

Lawyers for Mr Ablyazov accused the Italian authorities of arranging an “extraordinary rendition”. The interior ministry told The Independent it was making no comment on the events.

But following the Rome appeal court’s declaration that it was “perplexed” by the unusually rapid deportation of two relatives of a political refugee to a country with a dreadful human rights record, Prime Minister Enrico Letta announced he has ordered an internal inquiry into the affair.

Liberal Foreign Minister Emma Bonino was reported to be “furious” at the nature of the deportation and says she was not informed of events. In her official statement she said the deportations appeared “abnormal”. Justice Minister Anna Maria Cancellieri is also calling for clarification.

The fact 50 armed police were involved in the arrest at a villa near Rome on 29 May suggests the authorities had hoped to find Mr Ablyazov himself at the residence – and that they were expecting some resistance.

Britain granted Mr Ablyazov – a former energy minister under Nazarbayev – political asylum in 2011, after Amnesty International declared that he had been tortured for leading political opposition to the regime. But in June last year he fled the UK, apparently in order to avoid a jail sentence for lying about his financial assets.

Mr Ablyazov’s eldest daughter, Madina, speaking from Switzerland, told Radio Free Europe: “Probably, the minute they have him, they will just kill him. They want to kill him, because my father is the biggest opponent to the President.”

President Nazarbayev and President Alexander Lukashenko of Belarus head the only two European states denied participation in the Council of Europe because of their human rights records. Former premier Mr Berlusconi enjoys warm relations with both.