Samburu East sub-county Police Commander Juma Ombata was arrested on Tuesday after he was found ferrying rare sandalwood logs in a police vehicle.
Mr Ombata was arrested in Wamba, Samburu East, after officers acting on a tip-off intercepted the vehicle.
The suspect was to be taken to Nairobi to face charges, said Samburu County Commissioner Henry Wafula.
"The officer is being escorted to Nairobi by officers from the Serious Crime Unit. It is very unfortunate that he was engaging in such illegal activities. We cannot accept," Mr Wafula told the Nation.
He said a multi-agency team had intensified patrols in forests to combat illegal harvesting of sandalwood and other indigenous trees.
"We will not spare anyone found transporting the pieces of sandalwood because it is illegal. We will tame the illegal harvesting of the wood here in Samburu," he said.
Security agencies have been accused over the years of failing to end the illegal sandalwood trade, which has made unscrupulous businessmen overnight millionaires.
Police have been repeatedly fingered for collaborating with sandalwood dealers to fuel the illegal trade in Samburu.
The rare tree species is almost depleted and efforts to protect it have been futile.
Sandalwood could be on the brink of extinction as high demand abroad has triggered rampant felling of the trees. It is threatened in Baringo, Samburu, Kajiado and West Pokot counties.
The importance of sandalwood in traditional medicine, woodworking, rituals, pharmaceuticals and perfumes means there is high demand for it worldwide.