In a statement to newsrooms, Obonyo said the aircraft was returning from a combat mission in Jamaame, Southern Somalia.
“KDF aircraft while returning from a combat mission in Jamaame, (Southern Somalia), developed technical problems and crashed in the general area of Kismayu,” reads the statement.
The statement did not however state whether they were casualties.
Kenyan troops crossed into southern Somalia in 2011 to fight the Shabaab, later joining the now 22,000-strong African Union force battling the Islamists.
UPDATE Pilot of KDF aircraft that crashed in Somalia on Thursday said to be missing. Kenyan military says Al Shabaab set the aircraft on fire after it crashed due to mechanical problems.