Kenya sent soldiers into Somalia in 2011 after raids in the border region and kidnappings that threatened the tourism industry in the region's biggest economy and wider regional destabilisation.
It later joined the AMISOM operation.
Al Shabaab's attacks in Kenya have included a raid by gunmen on the upscale Westgate shopping mall in 2013 and a university in Garissa in 2015.
Kenya Defence Forces spokesman, Colonel David Obonyo, denied the number given by the Somali president and questioned the source of the information.
The al Qaeda-aligned militants have been driven out of major strongholds in Somalia by AMISOM and Somali army offensives, but the group still controls some rural areas and often launches guerrilla-style assaults and bomb attacks.
Al Shabaab, which wants to overthrow Somalia's Western-backed government, had initially said it had killed more than 100 soldiers in the attack.
-AAP