The move was intended to prevent attacks by militant Islamists from neighbouring Somalia, he said.
Police believe it will be easier to spot militants in vehicles with untinted windows, says the BBC‘s Robert Kiptoo in the capital, Nairobi.
Explosions on two buses in the city killed three people and wounded more than 80 earlier this month.
The government believes the al-Qaeda-linked al-Shabab group was behind the attacks.
Our correspondent says previous appeals by the authorities that coaches and minibus taxis – known as matatus – should not have tinted windows were ignored.
This is why Mr Kimaiyo has ordered their immediate seizure, though there are no reports yet of vehicles being impounded, he adds.
Many matatus have tinted windows and their owners will be under pressure to heed the order or risk confrontation with the police, our correspondent says.
Al-Shabab has carried out a spate of attacks in Kenya.
In September, at least 67 people were killed when its fighters seized the upmarket Westgate shopping mall in Nairobi for four days.
Kenya has vowed to halt the attacks and arrested some 2,000 people in Nairobi last month.