More than 800 soldiers have left the Kenya Defence Forces (KDF) since the Somalia operation began in 2011.
KDF Director of Prosecution Brigadier Kenneth Okoki Dindi told a Mombasa court that the soldiers left for various reasons, including desertion.
In a sworn affidavit filed at the Mombasa Court of Appeal, Brigadier Dindi said the departures had a direct effect on KDF's ability to check indiscipline and desertion among the soldiers.
KDF is seeking the court's permission fast-track proceedings of the State's appeal against the acquittal of 25 ex-soldiers from Mtongwe naval base in Mombasa.
The military court had jailed the soldiers - among those that had left KDF to work for US security firms abroad - for life after convicting them of desertion.
But on August 21 last year, Justice Martin Muya of the Mombasa High Court freed them, ruling that the military courts convicted them wrongly.