Thirty six suspected al Shabaab militants have been arrested in Operation Linda Boni which began nine months ago.
The suspects were handed to agencies including the ATPU for profiling and possible prosecution, said head of security operations James ole Serian.
He said on Tuesday that nine security stations comprising the military and members of the KWS and Kenya Forest Service will set up permanent base in the area.
Serian said the operation has been successful but that the terror group based in Somalia remains a threat. He also noted the reemergence of the Islamic State group in Somalia.
"Our security personnel are still holding the fort across the border," he said, and underlined the need for vigilance.
"Security at the border has been beefed up to ensure terror suspects do not penetrate into the country."
It emerged in July 2015 that al Shabaab militants had in the vast forest and were living there with their families.
The militants and their wives and children hunt game for food and use water from several rivers in the forest.
The disclosure came a day after militants ambushed a police van in Lamu, killed five people, including officers, with an improvised explosive device, and escaped.
In September that year, the Kenya Defence Forces and General Service Unit were of the forest.
The operation targeted the Jeysh Ayman, a 300-member al Shabaab cell that operated in the forest.
KDF reported the following month that it had ; military and police sources said most of the militants who had infiltrated the forest had abandoned the camps and fled to Somalia.
Early in March, six armoured GSU vehicles were dispatched to Lamu and the forest area to fight terror. The six are part of 30 vehicles the state imported to fight terror.
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On March 29, Serian said Lamu will soon be declared a following the success of Operation Linda Boni.