The attack on the Manda Bay airfield early on Sunday was the al-Qaida-linked group’s first attack against US forces in the East African country, and the military called the security situation "fluid" several hours after the assault.
Five attackers were killed, Kenyan military spokesman Paul Njuguna said.
Al-Shabaab, based in neighboring Somalia, claimed responsibility for the assault.
One US serviceman and two contractors with the US Department of Defense were killed in the fighting, according to a statement from the US Africa Command, or Africom.
Al-Shabaab claimed that there were 17 US casualties, nine Kenyan soldiers killed and seven aircraft destroyed.
Kenya is a key base for fighting al-Shabaab, one of the world’s most resilient extremist organizations. A large plume of black smoke rose above the airfield Sunday and residents said a car bomb had exploded. Lamu county commissioner Irungu Macharia told the Associated Press that five suspects were arrested and were being interrogated.
An internal Kenyan police report seen by the AP said two fixed-wing aircraft, a US Cessna and a Kenyan one, were destroyed along with two US helicopters and multiple US vehicles at the Manda Bay military airstrip. The report said explosions were heard at around 5.30am from the direction of the airstrip. The scene, now secured, indicated that al-Shabaab likely entered "to conduct targeted attacks", the report said.
The military’s Camp Simba has under 100 US personnel, according to Pentagon figures. US forces at the adjoining Manda Bay airfield train and give counterterror support to East African partners.