Jonathan had been scheduled to meet some parents of the victims, as well as five girls who escaped captivity hours after the attack in the remote town of Chibok in the northeast.
But a statement from the presidency, yesterday accused the activists, who started the Bring Back Our Girls campaign, of using the plight of the hostages "to play politics".
Some of the president's allies have claimed that the group is working with Jonathan's political opponents and exploiting the kidnapping to embarrass the government.
He is not known to have met with any of the girls' families.
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"Despite the shameful and disgusting games being played by the Nigerian chapter of Bring Back Our Girls, as a father of girls, I stand ready to meet with the parents of our abducted children," Jonathan said in the statement.
But campaign leader Hadiza Bala Usman told AFP that activists had simply asked to reschedule the meeting so that more parents could attend.
They "requested that the meeting with the president be shifted untill next week to allow for a larger representation", she said.
Malala, who survived a Taliban assassination attempt in 2012 and has become a champion for access to schooling, was in Abuja on her 17th birthday to mark three months since the Islamist rebels abducted more than 276 girls from a secondary school in Chibok.
At least 219 of the girls taken are still missing.
The Bring Back Our Girls campaign has drawn support from some of the world's most prominent personalities, including US First Lady Michelle Obama and actress Angelina Jolie.