"The decisions of the justice system must be obeyed and fully complied with," President Frei said in a radio and television address hours after retired general Manuel Contreras, 66, checked into hospital to avoid going to prison.
The president called on all Chileans to "place their trust in the rule of law, in democracy and in those of us who have the responsibility of government," adding that "nobody can prevent the Supreme Court from carrying out its sentence".
General Contreras had been holed up at his ranch in southern Chile, vowing not to go to jail, since the Supreme Court upheld on 31 May his conviction for the 1976 killing in Washington of the former Socialist foreign minister, Orlando Letelier.
Over the weekend General Contreras sought refuge in a Puerto Varas military barracks but then returned home, where the authorities tightened security awaiting an arrest order.
On Tuesday, he secretly boarded a military plane for Santiago with an army escort, but landed at Talcahuano, 250 miles south of Santiago, where he was whisked to a navy hospital.