The Catholic Church's Secretary of State, Cardinal Pietro Parolin, told US secretary of state John Kerry it was vital the facility was closed as soon as possible when the two men met.
Vatican spokesman Reverend Federico Lombardi said Cardinal Parolin expressed the Holy See's desire that "favourable attention" be paid to finding a solution for the inmates.
It's not the first time the Church has criticised the prison which is used to detain terror suspects.
Pope Francis spoke out about the need to protect prisoners' dignity and has criticised the policy of renditions used after September 11 2001.
It comes after last week's report into torture against terror suspects by the C.I.A.
A senior US State Department official said Mr Kerry "described recent progress in our diplomatic efforts to transfer detainees to third countries, including to Uruguay".