Steve Tikolo has replaced Robin Brown, who stood down after the side's failure to qualify for next year's ICC World Twenty20 championships in Bangladesh.
Obuya, a star of Kenya's 2003 World Cup semi-final success, was involved in an altercation with team-mate Irfan Karim during a recent tour of Sri Lanka.
All-rounder Collins Obuya was named as Kenya's new national cricket captain to replace Jimmy Kamande who was sacked after the disastrous 2011 World Cup campaign, Cricket Kenya said.