The magistrate said Monday he was satisfied with prosecutors’ evidence linking the three suspects to the days-long siege of Westgate Mall in which 67 people were killed.
A fourth suspect was freed for lack of evidence.
The Somali Islamic extremist group al-Shabab claimed responsibility for the attack that shocked Kenyans and horrified the world.
Since 2011 the rebel group, which is linked to al-Qaida, has vowed retribution on Kenya for sending troops to Somalia.