Blasts and exchange of fire rent the air for almost five hours.
Plumes of dark smoke billowed out of the Manda-Magogoni Naval Base in Lamu, in a scene straight out of the movies, with locals neighbouring the base keeping indoors.
Armed al-Shabaab militants had raided the Simba Base on Manda Bay Island, which also has US military presence.
The US marines regularly train their Kenyan counterparts at the base, which they have also used to launch aerial attacks against the Somali militants.
Around 5am on Sunday, an unknown number of attackers emerged from a small forest at Chandavai, accessed the Manda Airstrip in Lamu -- which is poorly-fenced -- before launching their attack that saw some equipment at the facility destroyed.
The raid brought back to the spotlight one of the country's top tourist destinations, whose vulnerability to militant attacks saw it suffer massive losses four years ago.
The Nation understands that the militants cut power supply in Hindi before gaining access to the base.
Reports indicated that some aircraft, which were not in use, are among the equipment the militants damaged.
Two hours later, the Kenya Defence Forces (KDF) aircraft responded in the attack of which al-Shabaab had claimed responsibility.
"We launched an attack at the US base that is home to hundreds of military personnel and serves as one of the many launch pads against us," the militants said in a statement.
The dawn attack comes barely a week after the US launched air strikes targeting al-Shabaab extremists after a car bomb killed at least 81 people in Somalia. Four militants were killed in the air strikes.
KDF spokesman Colonel Paul Njuguna said a fire that broke out during the Manda attack also affected some of the fuel tanks located at the airstrip.
He said five bodies of the al-Shabaab militants were recovered after the raid, which he termed as a failed attempt to breach security at the airstrip.
Sources told Nation that the bodies are those of suicide bombers from the al-Qaeda-affiliated terror group.
Col Njuguna further said there were no casualties or injuries of Kenyan soldiers and that the airstrip was safe.
"The attempted breach was successfully repulsed. Five terrorists' bodies have so far been found. The airstrip is safe," he said.
The US-Africa Command Centre confirmed the attack, adding that it was "monitoring the situation and would provide an update, as facts and details emerge".
"al-Shabaab is a brutal terrorist organisation," said US Army Maj-Gen William Gayler, US-Africa Command director of operations.
"It is an al-Qaeda affiliate seeking to establish a self-governed Islamic territory in East Africa; to remove Western influence and ideals from the region, and to further its jihadist agenda," Maj-Gen Gayler added.
Security sources indicated that the al-Shabaab attack targeted Manda-Magogoni Naval Base and the US military base dubbed Simba - both located on Manda Bay Island.
Lamu County Commissioner Irungu Macharia told the Nation that enough security officers, mostly the Kenya Navy within the camp and soldiers from other KDF units, had been deployed to pursue the attackers.
By 11am Sunday, Mr Macharia had confirmed the arrest of five individuals "linked to the attack", without providing details.
The attack saw the airstrip in Lamu closed temporarily, with the Kenya Civil Aviation Authority Director-General Gilbert Kibe saying they had "suspended civilian aircraft to that airstrip". The suspension was later lifted in the afternoon.
Locals interviewed by the Nation at Hindi town, which is about 20km from the naval Base, said they could hear gunshots and explosions coming from the direction of the camp.
"There is tension here at Hindi town since 5am. We could clearly hear gunshots from Manda-Magogoni. I think something isn't right there. We're praying for our gallant soldiers," said Mr Paul Mwaniki, a boda-boda operator.
The attack and killing of the five al-Shabaab militants came barely eight hours after a local reported sighting wounded suspected al-Shabaab militants in Kilelengwani on the neighbouring Tana River County on Saturday.
The local who was cutting wood for building in the nearby forest claimed to have been approached by about 11 wounded youths seeking medical help.
They were speaking fluent Swahili. According to the man, the militants even threatened to shoot him if he raised the alarm, but later let him go on condition that he would not reveal their presence in the area, which borders the Boni Forest.
Al-Shabaab militants have in the last four days undertaken daring raids that have left the region tense, with the naval base raid upping the stakes.
Four days ago, three people were killed while another three were injured when the militants ambushed a convoy of buses, including Simba Coach, Mombasa Raha and TSS that were headed to Lamu from Mombasa.
The attack happened on January 2 at Nyongoro area on the Lamu-Mombasa road.
On the same day, the regional multi-agency team announced that they had killed four militants who had taken part in this attack, and captured one alive, but details were not provided.
The Sunday dawn attack also comes at a time when security has been tightened across Lamu County, particularly along the Lamu-Mombasa route, even as fresh forced disappearance of suspected al-Shabaab sympathisers starts to emerge.
On Tuesday, a suspected al-Shabaab returnee was shot dead by unknown assailants while driving home.
Omar Salim Unda, 27, was shot three times in the head and neck at close range at Dabaso Primary School.
Unda is said to have undergone rehabilitation after returning from Somalia where he is suspected to have joined the group.
Recently, Coast Regional Coordinator John Elungata assured the Lamu-Mombasa road users and locals of their security.
"A contingent of security officers, including KDF and various police units, could have been patrolling the road. Operations against criminal elements and groups are continuing in Lamu under the county security committee which includes KDF," he said.