The suspects pleaded not guilty but the judge ordered they remain in custody.
They face three counts of murder for the deaths of lawyer Willie Kimani, Josphat Mwenda and their driver Joseph Muiruri.
The three went missing in June after Mr Kimani filed a case against a police officer on behalf of Mr Mwenda.
A week later, decomposing bodies of the three were recovered in a river, in the outskirts on Kenya’s capital Nairobi.
Post-mortem reports said the bodies had signs of torture.
The killings sparked outrage in Kenya and many have blamed the police force for a series of extrajudicial killings in recent years.
The hashtag #StopExtrajudicialKillings gained popularity on social media as people gathered to take part in protests around the country.
A joint statement by 34 Kenyan and international human rights organisations condemned the killings.
The government has denied the existence of police death squads, saying any killings are the work of “rogue officers”.
Kenyan security forces carried out 25 extrajudicial killing between 2013 and 2015, Kenya’s official rights body said.
However, non-governmental watchdog Independent Medico-Legal Unit (IMLU) says the police killed 97 people in 2015 alone.