The government said it was in touch with those claiming to be behind the undated video, which shows groups of girls in Islamic dress standing or sitting around a masked man armed with an assault rifle.
The film was issued just days after embattled Boko Haram head Abubakar Shekau denied claims he had been replaced as the leader of the Nigeria-based jihadist group.
The mass kidnapping of 276 schoolgirls from Chibok in April 2014 provoked global outrage and brought unprecedented attention to Boko Haram and its bloody quest to create a fundamentalist state in northeastern Nigeria.
"They should immediately release our brethren in their custody," the man said, warning that if the prisoners are not released the government will never be able to rescue the girls.
"They should know that their children are still in our hands," he said in the film posted on YouTube that appears to show some women injured after an air strike.
While President Muhammadu Buhari has said the group is "technically defeated", his government has struggled to find the girls, an enduring political embarrassment that highlights Boko Haram's continued presence in the region.
"There are a number of the girls, about 40 of them, that have been married," said the man in the 11-minute video. "Some of them have died as a result of aerial bombardment."
A girl speaking in the Chibok dialect chokes back tears as she describes an air strike by Nigerian armed forces.
In the background, several girls look visibly distressed and dab their eyes. One is holding a small baby.
"The video shows that the war effort is hurting the operations of the group," he said. "It does have a sense of almost desperation from Boko Haram."
The Nigerian government said it is in contact with those claiming to be behind the video but was acting cautiously given the leadership split.
"Since this is not the first time we have been contacted over the issue, we want to be doubly sure that those we are in touch with are who they claim to be," Information Minister Lai Mohammed said in a statement.
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