"The two women carrying infants... were not stopped, and exploded their own devices past the security point,” the report said.
Officials said the use of babies could signal a "dangerous" trend.
The incident took place just a few weeks after two girl suicide bombers blew themselves up, again at a checkpoint, outside the city of Maiduguri
The teenagers detonated their explosives when they were stopped for a search.
Three civilians were wounded.
Boko Haram has used scores of females in suicide bombings, with suspicions that most of these women would have been kidnapped.
The group's seven-year old Islamic uprising has killed more than 20 000 people.