Matiang'i, who is also Interior minister, has also asked traffic police to ensure the buses only operate between 6am and 6pm.
Last year, MPs passed Traffic (Amendment) Bill, 2016 which requires all school buses to be of this colour.
The Bill requires institution names written in black and that the vehicles have all prescribed signage. The law further proposes that the buses be fitted with safety belts designed for use by children.
These were part of changes aimed at improving the safety of pupils and teachers who use the vehicles.
Matiang'i raised questions about the low number of students who have reported to schools for the new term.
"I am alarmed by the low turn out of students reporting for form one in the coast region. I have spoken to governors ... together we must get more children to school."
The minister, who spoke at Kenya School of Government on Friday, noted marginalisation can only be fought through education.
"Parents and local leaders must ensure all children who are of age attend school without fail," he added.
Statistics show the region has recorded the lowest form one turnout following the 2017 KCSE examinations. Performance was poor.
In Kwale county, 754 learners reported yet 5,568 slots were available, while in Malindi, only 57 out of 240 places have been filled.
Haki Africa said on Thursday that Mombasa is recording an "alarmingly" low form one enrollment rate.
Executive Director Hussein Khalid added the county has generally been performing dismally in matters education because "officials are not serious".
The lobby group said while schools in other counties were hitting near 100 per cent turnout, Mombasa's best was 49.7 per cent - Mvita Secondary School.
A hundred and four of the expected 212 form ones went to school on Thursday, a week after schools reopened.
Earlier, Matiangi said those opposing the transfers of school principals will be arrested and prosecuted.
There has been uproar by members of the public and politicians following the transfers of 557 head teachers by the Teachers Service Commission.
In counties such as Bungoma, leaders have said they will set aside politics and protect the schools they worked hard to build.
One of these leaders is NASA principal, Senator and Ford Kenya boss Moses Wetang'ula.
In Makueni, five MCAs were arrested for blocking a new principal's access to her office at St Joseph's Girls' High School on Thursday.
LEWIS NYAUNDI