In an address published by the official Saudi Press Agency, Grand Mufti Shaikh Abd al-Aziz al-Shaikh told Saudis to consult knowledgeable religious scholars and ignore extreme interpretations of Islam.
"Some people call for jihad for the sake of God without justification," said al-Shaikh, adding: "Muslim youth must try and better themselves and their country but not through violence as Islam is not a violent religion, it is a merciful religion."
Riyadh has been working to quash armed opposition at home and improve the country’s image abroad - recently dismissing over 700 clerics and banning about 1,500 others from preaching for having a history of inciting dissent.
Senior clerics have also taken to the media to preach moderation among Saudis.
Some Islamists, including the Saudi born fugitive Usama Bin Ladin, have called the kingdom's ruling family infidels because of their ties to western governments.
The Saudi government blames al-Qaida for the Riyadh triple bomb attack in May which killed 35 people. Some 240 suspects have been arrested since then.
"Some people call for jihad for the sake of God without justification"
Shaikh Abd al-Aziz al-Shaikh Saudi Arabia's grand mufti
A sizeable illegal trade in weapons between Saudi Arabia and Yemen is likely to make the clampdown on armed groups more difficult.
Smugglers regularly supply arms dealers in Saudi Arabia despite both countries best efforts, a Saudi official said in comments published on Thursday.
Prince Muhammad bin Nasir bin Abd al-Aziz, governor of the Jizan province which borders Yemen, said Saudi border patrols seize arms caches on an hourly basis, but that some weapons are bound to slip through.
"This is no doubt a disturbing phenomenon that threatens our security … we are working with the Yemeni authorities to find and destroy the smuggling ring," Prince Muhammad told the Arabic daily Al-Sharq al-Awsat.
Earlier this week, Riyadh extradited four men to Yemen, including two suspected Islamists, believed to be linked to last year's attack on the French supertanker Limburg.
In June, the two countries agreed to co-operate closely on fighting weapons smuggling in the wake of the Riyadh bombings.