Witnesses told The Nation newspaper violence suddenly broke out in the Oshodi area around 9 p.m. Friday.
Internal disputes within transport unions were suspected of setting off the melee, and bystanders reportedly were assaulted, robbed and raped.
Casualty figures were unknown.
In Bauchi state in northern Nigeria, police said Saturday communal clashes in the Bogoro and Tafawa Balewa districts have claimed 16 lives, The Nigerian Tribune reported.
State Police Commissioner John Abakasanga said unknown attackers stormed some villages overnight.
The state government said: "All parties involved must accept a cease-fire and allow peace to reign. The demands of the people of these local governments can only be realized in an atmosphere devoid of chaos and rancor."
It also warned it "is fully prepared to deal ruthlessly with any person or groups with evil and satanic intentions."