The disclosure was made in leaked documents from Turkey's National Security Council (MGK), to a Turkish daily newspaper, Today's Zaman reported Monday.
The surveillance of individuals the government believed to be members of certain religious and faith-based groups largely focused on followers of Hizmet, a movement founded by Islamic scholar Fethullah Gulen.
Other religious groups that criticized the government also were monitored, reported the newspaper, Taraf.
The document demanded the government curb Gulen's activities by monitoring private schools, student housing, foundations and domestic and foreign activities.
The MGK document was endorsed in 2004 by a number of officials, including Prime Minister Recep Tayyip Erdogan and the foreign and justice ministers at the time.
Responding to the report, Omer Dincer, a senior member of the Justice and Development (AK) Party, said the document was never implemented. Dincer, who was Prime Ministry undersecretary in 2004, said the document published by Taraf was a remnant of the previous government concerned about "reactionary religious activities."
Dincer said the government headed by Mesut Yilmaz set up a council to monitor religious groups such as Gulen's, but the council was dissolved in 2010.
The Taraf report said a new department set up by the Prime Ministry continued to track the groups between 2011 and 2013.