Military spokesman David Obonyo said the troops had been trailing the suspects as part of Operation Linda Boni.
They laid ambush in Bodhei area of the forest where the five were killed.
"Those killed were part of the group that has been terrorizing peace-loving citizens in the area," Obonyo said.
"KDF assures the public that tracking of the rest of the terrorists will continue until the area is free from all threats posed by this group. We remain committed to our constitutional mandate of ensuring peace and security in our country."
Obonyo appealed to residents to report any suspicious individuals - with injuries or those seeking medical attention - to security teams.
The terror group has been carrying out sporadic attacks in several parts of the country following Kenya's contribution of soldiers to AMISOM.
Last month, a group of more than 30 heavily armed al shabaab militants descended on Silini, Mashambani and Bobo villages of Lamu West and beheaded four men.
The attack occurred exactly two years after the government launched the joint security operation to flush the militants out of the forest where they have set up bases.
Amid security operations, Coast regional coordinator Nelson Marwa has accused security operatives carrying out the operation of laxity.
Marwa has also accused chiefs and their assistants of taking bribes to allow the militants to operate in the area.
-The Star|JOSEPH NDUNDA