Gnassingbe met separately with the delegations in the presidential palace in the capital Lome, the sources said.
The Togolese presidency did not publish any statement on the meeting.
Mali's military junta in July called for the Togolese leader to mediate in the dispute.
Togo's Foreign Minister Robert Dussey last week visited Abidjan and Bamako to meet with Ivorian President Alassane Ouattara and Mali's transitional leader Assimi Goita.
The 49 Ivorian soldiers were detained after their arrival at Bamako airport on July 10.
Mali has called them "mercenaries", but Ivory Coast says they were sent to provide back-up duties for the UN peacekeeping mission in Mali.
A UN spokesman has said that while they were not UN peacekeeping troops as such, they were part of "national support elements" routinely deployed by contributing countries.
Mali is struggling with a long jihadist insurgency that has claimed thousands of lives and forced hundreds of thousands from their homes.
It is also in the grip of political upheaval after colonels angry at the government's handling of the insurgency seized power in August 2020.
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