"It's correct to say dozens of people were killed following the bomb blasts in Nyanya Bus Park this morning," Manzo Ezekiel of the National Emergency Management Agency (NEMA) told AFP on Monday.
The city has been attacked previously by Boko Haram insurgents, who say they are fighting to create a strict Islamic state in northern Nigeria.
"We have been able to bring some of the dead to the morgue and some injured have been taken to the hospital," said Charles Otegbade, head of search and rescue at the National Emergency Management Agency (NEMA).
An AFP reporter at the scene said there were signs of a major explosion, with the remnants of charred vehicles scattered in the area.
Some of the small shops at the station had been damaged or destroyed.
The private Channels television network showed images of thick black smoke billowing out from the station.
NEMA spokesman Manzo Ezekiel told AFP that the Nyanya station was crowded with people on their way to work in Abuja when the explosions rang out and that witnesses reported hearing two separate blasts.
Boko Haram is blamed for scores of attacks across northern and central Nigeria that have killed thousands since 2009.
