The Lagos State government yesterday said police had started an "aggressive manhunt for suspected militants" after the attacks in the Igbo-Olomu and Ishawo areas of the eastern suburb of Ikorodu on Friday.
"The gunmen, who were alleged to be from the Niger Delta, were said to have come in through the waterways close to the communities and started shooting sporadically," it added in an emailed statement.
The southern Niger delta region, which produces most of Nigeria's oil, has been hit since February this year by a string of attacks on pipelines and installations, severely hitting production.
The majority of attacks have also been concentrated in the states of Bayelsa and Delta.
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Lagos, in the southwest, only became an oil-producing state in May, when it began production from an offshore field. But Nigeria's financial hub is criss-crossed by oil and gas pipelines.
Lagos State police commissioner Fatai Owoseni denied some local media reports that as many as 50 people were killed.
"I can confirm that the casualty is six and no family till now has come out even while I was there to say that they have extra corpses," he told reporters on Saturday.
The state government deployed police and soldiers to the location last year because of repeated oil theft from pipelines - or "bunkering" as it is known locally.
Security has been stepped up to prevent attacks using boats via the nearby creeks, he added.