Riot police fired teargas to stop more than 100 members of the Mombasa Republican Council (MRC) from reaching the court to hear a case in which they are challenging the ban on their group.
Several protestors were arrested and one died after being hit by a stone.
“I can confirm the (victim) has just succumbed to injures,” Mombasa police chief Kipkemoi Rop said. “We are going to deal with members of the MRC ruthlessly.”
The MRC are demanding the secession of the coastal region from the rest of the country, arguing that the area has been neglected by the central government and have repeatedly claimed that the Mombasa region is not part of Kenya.
Kenyan Prime Minister Raila Odinga, who has called for dialogue with the group, this week said the MRC must denounce its separatist claims before talks.
Yusuf Lule, an official with the Muslim Human Rights group, condemned the clampdown on the MRC.
“There is freedom of gathering, and police should not disperse innocent Kenyans” Lule said.
The Mombasa region is predominantly Muslim. The MRC has lodged a case to have the ban reversed.