Joseph Kanyiri, director of Operation Linda Boni (Swahili for Operation Protect Boni), who has been overseeing operations to flush out the militants in the vast Boni forest, said some youth fleeing Somalia are part of the Al-Shabaab elite squad Jaysh Al-Ayman that comprises mainly Kenyans.
Kanyiri said more than 100 Islamist militants were killed on Tuesday at a camp 200 km northwest of Mogadishu, the Somali capital.
In March 2016 more than 150 fighters were also killed in similar airstrike by the United States.
Kanyiri said a multi-agency team has scale up security along the Somali border to deal with fighters who are fleeing from Somalia.
"We are aware the condition in Somalia is not conducive for them and they have decided to flee Somalia to the country. We urge them to surrender to authorities," said Kanyiri.
He said the ongoing Boni enclave campaign has also affected the Al-Shabaab operation inside Somalia after security agents managed to flush them from the vast forest by destroying their camps.
Over 300 members of the group had operated from the forest since 2012 to launch attacks against Kenyan troops.