The accident happened at a bus stop in the Ikeja area of Lagos, a city of around 20 million people, Lagos state emergency services said in a statement.
The country’s President Muhammadu Buhari described the accident as “distressing and extremely sad,” in a statement on Thursday.
Security guard Ubong Okon witnessed the aftermath of the crash, which happened from about 7 a.m. to 8 a.m. local time (0600 to 0700 GMT).
“I came out to open the gate, then I saw the train and the bus, I looked inside the bus, there were lots of passengers inside, I went inside and saw people with injuries, there was blood everywhere, then I started to help get people inside the bus out.”
Traffic jams are part of daily life in Lagos, where most people drive with little regard for road and safety rules.
In Africa’s most populous nation, many roads are poorly maintained and riven with potholes, leading to accidents that claim thousands of lives every year.
Aviation Minister Hadi Sirika said in a statement that he has directed Nigeria’s safety investigation agency to look into the cause of the accident.