Tough security measures have helped curb the violence but analysts and diplomats say radical Islamic ideology and anger at Western policy remains strong in the kingdom.
Prince Nayef urged the official religious establishment to avoid the spread of extreme views.
"If there is no efficient and positive action from our scholars, clerics, mosque imams, thinkers, newspapers and television channels to develop and strengthen ideological security, we will have a deficiency," he said.
Last week, Prince Nayef said that the "virus" of extremism was still alive in Saudi Arabia despite its success in curbing attacks led by al-Qaeda sympathisers.
The interior minister's comments came after a man suspected of involvement in the killing of four Frenchmen was shot dead by security forces.
Waleed bin Mutlaq al-Radadi died in a gun battle north of Medinaon Friday, the kingdom's news agency said.