Reports said government chartered plane conveyed the parents and others to the meeting attended by more than 150 people.
Before he conveyed the meeting, President Jonathan has been under pressure from interest groups, both local and foreign, including the opposition party, to meet with parents of the abducted girls.
Some of the parents reportedly pulled out of a meeting earlier called by the President last week amid accusations they were being used for political reasons, a BBC report said.
The parents of 11 of the girls have died since their abduction by the Boko Haram group, the Associated Press news agency reports.
The abduction of the more than 200 schoolgirls sparked global outrage.
Boko Haram has offered to free the girls in exchange for the release of its fighters and relatives held by the security forces.