"The death toll is now six - four females and two males," Ibrahim Farinloye of the National Emergency Management Agency (NEMA) told AFP, revising an initial toll of two.
He said 74 people were injured, with some in critically.
"The death toll might rise further because a lot of people are in critical condition in the hospital," he said.
Farinloye said emergency workers struggled for hours before they could rescue people trapped in the wreckage of the bus, which was left mangled at the front of the train.
The train had been travelling from Ijoko in nearby Ogun state and heading to Ebute-Meta area in Lagos. The crash took place in the PWD area of the city of more than 20 million.
NEMA blamed the bus driver's "reckless driving" for the crash, accusing the driver of "trying to beat the train traffic signal before the moving train rammed" into the vehicle.
Accidents are common on Nigeria's poorly maintained roads as a result of speeding, reckless driving and disregarding traffic rules.
Most motorists spend several hours daily locked in traffic in the metropolis and the Nigeria Railway operates daily passenger train services in the city.