In a statement, director general Gilbert Kibe said the staffer, an aerodrome control officer, jumped from the tower on Friday under unclear circumstances.
Kibe said the staff is working with the authorities to investigate the incident.
"The board and management stands with all the air traffic control officers during this time, having lost a valuable member of the team," the statement said.
This comes as a Kenyan doctor in Cuba allegedly committed suicide in Cuba.
Hamisi Ali's body arrived in Kenya on Friday and was buried according to Muslim customs.
Ali was the brother of Malindi MP Mishi Mboko.
The family said it would seek an independent autopsy.
Kenyan doctors in Cuba have complained about harsh living conditions in the country, forcing the Health ministry to review their terms, including salary.
PS Susan Mochache said they will now earn an additional Sh144,000, up from the Sh50,800 they earned.