Mokotjo was called up to the national team by stand-in coach Owen da Gama, ahead of back-to-back friendlies against Guinea-Bissau and Angola, marking an end to his temporary retirement.
The 26-year-old is currently in camp with the team in Durban, but it is as yet unknown whether he will be able to play as he no longer holds a South African passport.
The FC Twente midfielder last year renounced his South African citizenship as part of the legal practice of naturalisation to become a Dutch national after living in the Netherlands for more than five years, forcing him to hand over his SA documents.
However, in a bid to now obtain dual citizenship and get Mokotjo a new SA passport, SAFA have turned to Home Affairs to resolve the issue, with the custodian saying they have placed the matter under "utmost urgency".
"The Department of Home Affairs wishes to confirm that we are in contact with the South African Football Association (SAFA) pertaining to the citizenship of Netherland-based soccer player, Kamohelo Mokotjo, who has taken up the Dutch citizenship through naturalisation," read a statement released on Wednesday.
"Further to this, we have contacted the Dutch authorities with a view to resolving this issue within the legislative prescripts in the two countries.
"Mokotjo has been called to represent South Africa during the upcoming international friendly soccer matches against Guinea-Bissau and Angola and has expressed his desire to represent his country of birth.
"The Department of Home Affairs is treating this matter with the utmost urgency and we will provide an update soonest on the developments in this regard."
Bafana take on Guinea-Bissau at the Moses Mabhida Stadium on Saturday afternoon (15h00) before hosting Angola at the Buffalo City Park Stadium next Tuesday (19h00).