The attacks by the Army, Air Force and Navy, began on Thursday night under the operation “Crocodile Laugh” in readiness for a confrontation with militants in the Niger Delta.
The Director of Defence Information, Brig Gen Rabe Abubakar, confirmed the operation.
He said it was conducted to flush out militants and saboteurs from the area.
The attacks reportedly sent the local residents scampering, but they have been assured of safety and advised against sheltering any of the fleeing militants.
The creeks in Lagos and Ogun states recently became a safe haven and operational hideout for militants from Niger Delta.
Besides oil pipeline vandalism and petroleum theft in Arepo in Ogun State and parts of Lagos, the militants have been attacking innocent residents and stealing from them.
Military analysts say the dislodgment of the militants was carried out to drive them back to the Niger Delta where a full scale attack was imminent.
Militants have in the last three months inflicted massive damage on the economy through the destruction of gas and crude oil pipelines.
Lagos police spokesperson Dolapo Badmos also confirmed the operation in a statement released early Friday.
“We are sweeping through the waterways where we share boundaries with Niger Delta to end the activities of the militants,” she said.
Meanwhile, the Governor of Bayelsa, Mr Seriaki Dickson, met with President Muhammadu Buhari on Thursday to ask for more time to initiate dialogue with the rampaging militants.
The Niger Delta Avengers have refused entreaties from government and have insisted on autonomy for the region or complete control of crude oil.
The Avengers, who emerged in May 2016, did not give the new government prior notice before embarking on massive destructions of oil and gas infrastructure. They have also resorted to killing and kidnapping of security personnel.