General Mansour al-Turki, the interior ministry spokesman, said that 10 or 11 of those released are believed to have re-joined al-Qaeda in Yemen.
Another four have been killed in operations against al-Qaeda and the remainder have been rearrested, al-Turki said.
The men were held at the US detention centre in Guantanamo Bay, Cubaafter Washington launched its so-called "War on Terror" following the September 11, 2001 attacks on the US.
Most of the September 11 suicide hijackers were of Saudi nationality.
Three former Guantanamo detainees currently remain in the Saudi programme, which uses religious re-education by clerics and financial assistance to help detainees start a new life.
About 300 people have gone through the programme, which was established in response to attacks by al-Qaeda in Saudi Arabia from 2003 to 2006.
Al-Hadlaq cited strong personal ties among former Guantanamo prisonersand tough US tactics as the reason why some of the former detainees relapsed into violence.
"Those guys from other groups didn't suffer torture before the non-Guantanamo [participants]," al-Hadlaq told reporters in a rare briefing about Saudi anti-terrorism efforts.
"Torturing is the most dangerous thing in radicalisation. You have more extremist people if you have more torture."
However, al-Hadlaq said that the programme had been a success so far and that the government was still planning to expand it with new facilities in five cities.
Another 13 Saudis are still held in Guantanamo Bay.