Aviation regulator says airlines used passenger planes to carry cargo.
The Kenya Civil Aviation Authority (KCAA) has withdrawn licences of two airlines which violated permit rules.
The Wilson Airport-based airlines, which are licensed to carry passengers, have been illegally ferrying cargo without the clearance from the regulator.
"It is true we have grounded the two airlines for defying the set rules," said KCAA director-general Gilbert Kibe without revealing their identities.
Mr Kibe says the airlines had removed seats on the aircraft to create space for cargo.
He did not give details on cargo being ferried from Wilson Airport, but pointed out that miraa (khat) forms part of the cargo that is transported.
Kenya mainly exports tonnes of miraa daily to Somalia through the airport.