Saudi Interior Minister Prince Naif bin Abdul Aziz said in a statement the campaign was aimed at undermining the country's lifestyle and economy and had a direct link to al-Qaida, the Saudi Press Agency reported.
"Each case will be examined in stages," the minister said.
In addition to the 991 indicted Tuesday, Naif said others would be would be indicted and tried.
Militants carried out more than 30 operations inside Saudi Arabia during several years, killing 74 security personnel and injuring 657 other law enforcement officials, Naif said. The operations also killed 90 civilians and injured 439 others, which include Saudis and foreigners.
Saudi Arabia began an aggressive anti-terror campaign in May 2003, when al-Qaida-affiliated militants began attacks against foreigners, oil installations and security forces, reported KUNA, the Kuwaiti news agency.