Coast Regional Coordinator Samuel Kilele warned that no vehicle would be allowed to operate on the route past 6pm.
The highway is situated along the vast Boni forest where militias are believed to be hiding.
Kilele said the move was meant to enable security agencies hunt down gunmen behind the continued Lamu killings, with latest being Friday night’s attack that left seven people dead.
Among the seven victims were four police officers, two passengers and a driver who were shot when gunmen ambushed a three-vehicle convoy.
The two passengers succumbed to injuries while undergoing treatment on Saturday morning.
Lamu County Commissioner Njenga Miiri said the policemen were escorting the convoy when the attack occurred.
“We have seven people dead in Friday attack. We are pursuing the assailants,” Miiri said.
Some of the passengers were said to be missing in the aftermath of the attack and it was not known whether they had been abducted or fled in panic.
The attack comes days after Kenya Defence Force destroyed military camps in Boni forest where the militiamen behind the killings are believed to be hiding.
Lamu has been hit by a series of attacks since mid-June which, according to the Kenya Red Cross, has left over 90 people dead.
The attacks have fuelled divisions on the coast, a region where radical Islam, ethnic tensions and land disputes are an explosive cocktail.
Somalia’s Al-Qaeda linked Shabaab have claimed responsibility for some attacks, saying they were in retaliation for Kenya’s military presence in Somalia as part of the African Union force supporting the country’s fragile government.
However, police and government officials have blamed the Mombasa Republican Council (MRC), a group that campaigns for independence of the coastal region.
This comes as the latest security measure by the Government after a chain of attacks in Lamu County despite heavy police presence in the area.