The strike earlier this month targeted a camp where the Kenya Defence Forces said the Amniyat, Al-Shabaab's intelligence wing, was training around 80 recruits.
Mahad Mohammed Karatey, also known as Mahat Karatey, was killed along with 10 mid level Al-Shabaab commanders and 42 recruits, said the KDF, which is part of the African Union peacekeeping mission in Somalia.
He was attending a graduation ceremony for the recruits, the KDF said.
The U.S. Department of State has designated Karatey as a terrorist and is offering up to $5 million for information locating him.
But Al-Shabaab contradicted the KDF on a radio station sympathetic to their cause -- Radio Andulus -- saying "Al-Shabaab denies that any airstrike targeting Al-Shabaab has taken place. The intention of Kenya is to divert attention from El Adde, [Somali,] where hundreds of Kenyan troops died."
A suicide bombing attack struck an African Union base there in January.
In addition, a Somali intelligence source told CNN that officials do not believe that Karatey is dead. They also believe an Amniyat training program would never involve so many people.
Karatey is known as a high-level Al-Shabaab commander of the Amniyat.
Kenyan and U.S. authorities believe Karatey was directly involved in the attack on Garissa University in Kenya last year, which killed 148 people. Most of them were students.
Authorities also believe Karatey had a hand in the El Adde attack.
Al-Shabaab most recently claimed responsibility for the failed bombing of a Daallo Airlines flight departing Mogadishu in early February. The explosion killed only the bomber and injured two others. But the bomb, said to be sophisticated, was believed to be hidden in a laptop.
Al-Shabaab is fighting a guerrilla war in Somalia with the intention of imposing Sharia law. It has also regularly carried out attacks with multiple casualties in Kenya and has sworn revenge for that country's military participation against the terrorists in Somalia.
The terror group is officially affiliated with al Qaeda, although last year a fraction
pledged allegiance to ISIS.