Lamu County Police Commander Muchangi Kioi has been transferred.
Irungu Macharia, the county secretary has confirmed. His new station is yet to be revealed.
Mr Macharia said the transfer is a routine exercise which has nothing to do with insecurity in the area.
There have been two recent terrorist attacks in the area. Last year, an administrator and a police officer were killed.
"This is just a normal transfer. It has nothing to do with insecurity," Macharia said.
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Mr Kioi has been replaced by Issa Mohammed who has been the Changamwe sub-county police commander.
In the Al Shabab attacks, six people were killed earlier this month.
The terrorists targeted commuter buses and an American military base in Manda Bay.
Lack of coordination between local government administrators and junior police officers has been blamed for the attacks.
Last month, Mohammed Famau, a chief, and his assistant Malik Athman, were butchered by unknown assailants inside their offices.
Hesbon Okemwa, a police officer attached to Tchundwa Police Post, was killed in cold blood by suspected drug barons and his riffle stolen.
His mutilated body was later recovered in a thicket.
Police sources said Mr Mohamed, who was at one time in charge of the coast region anti-terrorism police unit, was proposed by his seniors to head the terror prone area.