The Kenya Defense Forces (KDF) on Sunday morning confirmed the attack at Camp Simba in Manda Island, Lamu County.
The military base hosts elite US Marine and KDF troops and it is situated along Kenya-Somalia border in the Indian Ocean.
KDF spokesman Col Paul Njuguna on Sunday said the attack was successfully repulsed, adding that close to four suspected Al-Shabaab militants had been killed.
Manda Airstrip, Col Njuguna said, has since been secured, adding that it was an attempted breach of security at the base.
"This morning at around 5:30 am an attempt was made to breach security at Manda Air Strip. The attempted breach was successfully repulsed. Four terrorists bodies have so far been found," he said in a post on Facebook.
"The airstrip is safe. Arising from the unsuccessful breach a fire broke out affecting some of the fuel tanks located at the airstrip. The fire has been put under control and standard security procedures are now on-going."
The militants raided the camp on Sunday morning, the second attack in Lamu County within a span of two days.
Al-Shabaab claimed: "In early morning on Sunday, an elite group of soldiers from Harakat Al-Shabaab launched a daring dawn raid at a US Naval base known as Camp Simba."
The militants also claimed that both Kenya and the US suffered heavy casualties during the raid, which comes a day after the US killed a top Iranian commander.
However, Al-Shabaab did not confirm the alleged numbers of soldiers affected during the "successful raid" that targeted Americans.
"Fighters covertly entered the enemy lines, successfully stormed the heavily fortified military base and have now effectively taken control, inflicting casualties on both American and Kenyan troops," read the statement.