Earlier on Saturday morning a bus taking people to the capital Nairobi for the Christmas period was stopped by the Muslim extremists.
The militants ordered passengers to read a passage from the Koran and shot dead the 28 that could not.
A number of Muslims pled with the gunmen not to kill Christians but they too were shot.
Other Muslims were freed.
Senior adviser to President Uhuru Kenyatta, Abdikadir Mohammed, said: "The aim is to create conflict between the Muslims and the non-Muslims in this country."
He told the BBC it was an attempt to create 'a religious war, religious strife, in Kenya'.
Survivors have said the driver tried to accelerate away from the scene but his vehicle got trapped in mud.
Kenyan authorities have pledged to track down the fighters and bring them to justice.
Local media reported that the country's military had destroyed an Al-Shabab camp and killed 'many'.
Mr Mohammed added: "We have had a lot of the Muslim leaders come out today [Saturday] and strongly condemn this and call on Kenyans of all faiths and creeds to stand together against these heinous crimes and criminals."