The KDF has reported killing Mohammed Karatey aka Mahat Karatey, who headed al Shabaab's intelligence wing,
in a major strike on Nadaris camp in Somalia last Monday.
The Defence ministry said KDF soldiers under Amisom killed the commander, who was also the militant group's deputy commander, alongside 10 other mid-level commanders.
"Karatey had gone to the camp to preside over the passing out of an estimated 80 Alamnyat recruits who had completed their training and were due for deployment," the ministry said.
"It is confirmed that 42 recruits were also killed [in the attack between Buale and Sukow] while many others sustained injuries."
The Alamnyat intelligence wing
is made up of suicide bombers, assassins, explosives experts and information gatherers.
The ministry said it is believed Karatey played a key role in the January 15 attack on a camp in El Adde that left dozens of Kenya Defence Forces soldiers dead and some reportedly .
The slain commander is said to have deployed suicide bombers to the location for the attack described as the worst since Kenya joined the peacekeeping mission in 2011.
"His killing adds to that of Abdi Dek, the operation commander of the Abu Zubeir Brigade that carried out the attack in El adde," read the statement.
The ministry assured the fight against the al Qaeda-linked militants will continue until justice is acquired, and that Kenyan soldiers are committed to the Amisom mandate to restore peace and security in Somalia.
But al Shabaab said the commander was still alive.
Sheikh Abiasis Abu Musab, al Shabaab's military operation spokesman, said the group's fighters were targeted by a bombing, but that Karatey was alive.
"Mahad Karatey is alive and healthy," Abu Musab told Reuters by telephone.
The African Union Mission in Somalia, though authorised to have up to three military attack helicopters, has none. This raises questions on whether troops serving in the force could have carried out the air strike.
Official details of the El Adde attack have not been released. On Wednesday, Cord leader Raila Odinga asked the government to issue a comprehensive statement.
Raila said Kenyans should be who died as they defended the nation and deserve to be honoured and remembered.