A group of protesters wielding sticks descended on the court entrance after a ruling that the accused officer could take part in the hearings via video link, prompting police to intervene.
Several protesters were injured and 18 detained.
Ankara police declined to confirm the arrests and the crowd was later dispersed after riot control officers moved in.
Officer Ahmet Sahbaz is accused of killing Ethem Sarisuluk, who was shot dead in June during a wave of nationwide anti-government demonstrations set off by a tough police response to a protest over the redevelopment of a park in Istanbul.
Six people, including a police officer, died during the weeks of unrest, which presented one of the biggest challenges to Prime Minister Tayyip Erdogan's decade-old rule and caused alarm among Turkey's western allies.
Demonstrators, some armed with rocks, fireworks and petrol bombs, fought police firing tear gas, water cannon and pepper spray night after night, with the worst of the violence in Istanbul and the capital Ankara.
Amnesty International said earlier this month Turkish authorities had committed widespread rights abuses during the unrest, beating and harassing protesters.
Turkish officials have defended the police response and said such abuses will be investigated.
The court hearing was adjourned until Monday, December 2.