This is the second attack that the group that has links to Al-Qaeda has carried out this week.
The attack comes exactly one year after al-Shabaab said it had killed more than 100 KDF soldiers in El Adde, a Somali camp near the border with Kenya.
Kenya contributes more than 3,600 troops to the 22,000-strong AU mission in Somalia, which is helping the government fight al-Shabaab.
"An intensive pacification operation is under way, reinforced by our air and land forces", the statement added.
On Saturday, Defence Cabinet Secretary Raychelle Omamo and senior military officers visited the Defence Memorial Hospital to comfort the recuperating soldiers as well as address the next of kin of the dead soldiers.
In January past year a Kenyan base at El-Adde was attacked and overrun by Shabaab fighters who claimed to have killed over 100 Kenyan soldiers. The first batch of bodies of the KDF soldiers killed in Somalia's El Adde region were received on Monday.
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"We have now established beyond doubt that tens of our soldiers died on the line of duty in Somalia following the attack by militants", Raila said.
A spokesman for al Shabaab, which often launches attacks on troops of the African Union's AMISOM force, said its fighters killed at least 66 Kenyans at the base in the southern town of Kulbiyow, near the Kenyan border.
"It was a bad scene", one of the officers told The Standard, a local daily, on Sunday, adding that the attack closely mirrored last year's ambush at El Adde, where 173 soldiers were killed.
"Two mujahideen (fighters) rammed suicide auto bombs into the base in Kulbiyow town before storming it", he said, adding that as well as counting 57 Kenyan bodies, the group seized vehicles and weapons. The militants typically ram the entrance to a target site with a auto or truck so fighters can storm in.
The attack started when a truck filled with explosives detonated at the base, followed by heavy gunfire and an infantry attack.
However, Njuguna said KDF soldiers at Kulbiyow camp remain vigilant and undeterred and will ruthlessly pursue the insurgents to stabilize the Horn of Africa nation.