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The EUobserver said Friday that Usackas' resignation comes after the foreign minister and President Dalia Grybauskaite were engaged in a public dispute over Lithuania allegedly holding prisoners at a secret CIA prison.

While Grybauskaite suspected prisoners were previously held in Lithuania in secret, Usackas denied Lithuania used a CIA prison for such detainees.

The dispute by the two officials led to a parliamentary inquiry that found secret services in Lithuania had operated prisons with the CIA between 2002 and 2006.

The inquiry did not result in confirmation that prisoners were held at the facilities operated with the assistance of the U.S. intelligence agency, the EUobserver said.

On Thursday, Usackas spoke with reporters about his resignation.

"I've signed my letter of resignation and I'll present it to the prime minister today. I am confident that Lithuania's diplomatic service will satisfy the expectations of the citizens and will vouchsafe the expression of country's national interests, independent of any change of personality", he said.

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