A Saudi Arabia prosecutor has demanded the death sentence by crucifixion of a prominent Shia cleric who was arrested last year, prompting deadly protests in the Gulf kingdom.

Sheikh Nemer al-Nemer, a firebrand preacher seen as a radical leader in the Shia minority, was accused of inciting sectarian strife, "aiding terrorists" and instigating them to commit crimes and interfering in the matters of neighbouring countries.

The prosecutor said he was guilty of "waging war on God", a crime that automatically carries the death penalty according to the sharia. Earlier this month, 16 Shiites were detained on charges of spying for Riyad's rival Iran. Teheran has denied any allegations of spying in the kingdom.

In the past two years, clashes between police and protesters in the Saudi's Eastern province of Qatif, a Shiite-dominated area, have led to 16 demonstrators and a security officer being killed. Nemer was based in al-Awamiyah, a neighbourhood in Qatif that was at the centre of the unrest. He was detained in July 2012 after a car chase. Police said he had rammed a police car and possessed weapons. But local Shiite denied both accusations. After his arrests, three demonstrators were killed during protests.

Nemer was indicted for meeting some of the people that featured in a list of 23 wanted over the unrest in Qatif. They were accused of being foreign agents from Iran. The cleric was also accused of interfering in the internal affairs of Bahrain.