The much anticipated meeting comes amid reports of a worsening security crisis in the northeast, where Islamists have occupied the town of Damboa and surrounding areas, with the military so far unable to chase them out.
The girls were kidnapped from a secondary school in Chibok in the northeast on April 14 and carted away in a convoy of trucks. Of the 276 girls seized in the nightime raid, 219 are still missing.
His office tried to organise a meeting in the capital last week with a small group of the affected families, after he was urged to do so by the Pakistani activist Malala Yousafzai.
Malala, who survived a Taliban assassination attempt in 2012, was in Abuja on her 17th birthday to campaign for the girls' release.
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The families balked at the invite, saying that if Jonathan was unwilling to travel to Chibok, he should bring all of the relatives to his office to meet with them as a group.
Aside from parents of the hostages, the delegation includes some of the 57 girls who escaped their Islamist captors as well as Chibok community leaders, a source at the presidency said on condition of anonymity.
After a brief prayer delivered in front of the media, the group entered closed door talks.
Ayuba Chibok, who has two nieces among the hostages, told AFP that the government chartered a plane from Yola in the northeast to fly to the group to the capital yesterday.
Western powers, including the US, have offered logistical and military support to Nigeria's rescue effort, but there have been few signs of progress so far, despite assurances from officials that the crisis would soon be resolved.