Ali Salem Tamek was arrested on Monday upon his arrival from Europe at Laayoune airport in Western Sahara, a Moroccan government source said.
"His name has been mentioned several times during interrogations of rioters arrested after the events of Laayoune in June. He has been encouraging and instigating trouble via telephone from Europe during the events," the source said.
Tamek was freed last year under an amnesty by King Mohammed VI after spending nearly 15 months in jail over his alleged support for the Algeria-backed Polisario Front, which seeks independence in the northwest African desert territory.
He has over the past year given interviews to local and foreign newspapers indicating his support for the independence of Western Sahara through the long-delayed referendum plan proposed by the United Nations.
Tamek will be brought before the courts once the inquiry has been completed, Morocco's official MAP news agency said.
Morocco annexed Western
Sahara in 1975
"It's a normal procedure. He will be interrogated by criminal police upon order of the king's prosecutor," said the government source, who declined to be named.
Friends who waited for him at the airport said he was quickly whisked away by the authorities from the plane, which arrived from Las Palmas.
Six Western Sahara residents were sentenced last month to jail terms of one to five years for taking part in anti-Morocco riots. The mineral-rich territory has seen an escalation in clashes with the authorities in recent months.
Morocco in 1975 annexed the former Spanish colony in a move that was not recognised internationally, sparking a guerrilla war with the Polisario Front.
A UN ceasefire was brokered in 1991 with the promise of holding a referendum to decide the fate of the area, believed to have offshore oil deposits. Disagreements about who is eligible to vote have prevented it from taking place.
In recent years, Morocco steered clear of the independence option and stated its readiness to grant the area only semi-autonomy while remaining under its sovereignty.
The Polisario Front pledged in May to resume its armed struggle against Morocco if there was no breakthrough in UN-led peace talks within six months.