The teachers, who have been charged with subjecting the Grade Two students to cruel, inhuman and degrading treatment and punishment, "took a plea of not guilty," their lawyer Edward Begi told AFP.
"They were released on a bond of 500,000 Kenyan shillings ($4,000) each," he said.
The Teachers Service Commission suspended the six teachers last week, saying the video caused "trauma, psychological, mental torture and embarrassment to the minors."
The incident sparked fury on social media and calls for action in the largely conservative, Christian nation.
Education Minister Ezekiel Machogu said the teachers would face disciplinary action and would be dismissed if found guilty.
The five men and one woman were arrested last week after a video of the punishment went viral, showing four uniformed boys simulating sexual acts in the school compound while their teachers watched.
The teachers are heard chatting in the background of the 29-second clip and bursting into laughter as one shirtless child wipes tears from his face.
Police said the video clip was recorded in Nyamache, a rural town around 300 kilometers east of the capital, Nairobi.