Skyward Express is among five airlines that will face punitive action from the sector regulator until they address regulatory breaches.
The move by the Kenya Civil Aviation Authority (KCAA) will also affect Buff Air, Capital Airlines Limited, Bush Air and Rudufu.
The five airlines, which operate from Wilson Airport mainly to Somalia, are accused of violating airworthiness registration.
They are also accused of using their aircraft in transportation of cargo when they are not licensed for that purpose.
“There is no shortcut to this, they just shave to conform to the set standards,” said a KCAA official.
Transport secretary James Macharia said passenger airlines that violate their licences will be dealt with firmly.
“The airlines that were intercepted were licensed to carry passengers only not to also operate as cargo airlines which is contrary to the licence conditions,” said Mr Macharia during the launch of the new airport charter last month.
Mr Macharia urged agencies charged with licensing the airlines to take firm action on airlines contravening regulations.
This was revealed after a team of investigators had been deployed to probe claims some aircraft operators at Wilson and Jomo Kenyatta International airports violate cargo carriage rules.
Kenya received category one status in 2016 a move that would allow airlines that have been certified by the US aviation regulator to fly directly to America. It is feared that such a move by airlines to violate their airworthiness registration might affect the country’s quest for direct flights between the two countries.
The US transport agency wants Kenya to carry out corrective measure on some of the security measures before JKIA gets the last point of departure status to allow for direct flights between Kenya and America.
Editor's note: The story has been edited to remove references to revocation of licences. The headline has also been revised to reflect the changes.