Obasanjo said President Goodluck Jonathan's administration had taken too long to respond to the mass abduction.
"I believe that some of them will never return. We will still be hearing about them many years from now," Obasanjo told the BBC's Hausa-language radio service on Thursday, in comments echoed in an interview with Nigeria's Premium Times website.
The warning from Obasanjo, who stepped down in 2007 but remains an influential figure, will dismay parents who have now waited 60 days for any news of their daughters, taken from a school in the village of Chibok on April 14.
Obasanjo's criticisms underline divisions within Jonathan and Obasanjo's ruling People's Democratic Party, heightened by the government and army's failure to rescue the girls, and by presidential elections due in 2015.
"If you get all of them back, I will consider it a near-miracle ... Do you think they (Boko Haram) will hold all of them together up till now? The logistics for them to do that, holding over 200 girls together, is too much," Obasanjo said, according to Premium Times.
"If the administration had acted quickly, we could have rescued them," he said.