Five nations are still in line to take the two African berths at August's Fifa Under-20 Women's World Championship.
The African race to Russia will be decided next month when plays-offs are held between South Africa and Liberia, while Nigeria will take on either DR Congo or Mali.
Mali were supposed to travel to Kinshasa this weekend to contest the second leg but never made it.
"We are waiting for a report from our match commissioner before commenting on the Mali situation," said Suleiman Habuba, a spokesman for the Confederation of African Football (Caf).
"Only then will we know why they did not get to the venue."
It is understood that the Malians, who drew the first leg 1-1, may have had logistical difficulties which prevented them from flying.
Whether DR Congo or Mali play Nigeria in the play-off, they will face tough opposition.
The Nigerian Eaglets beat Kenya 10-1 on aggregate, winning the second leg 2-1 in Nairobi on Saturday.
South Africa also made it through in style, winning 3-0 in Mozambique to clinch a 9-0 aggregate victory.
They next face Liberia, who qualified after their opponents also failed to show up.
Caf says Algeria, who lost the opening leg 3-2, have officially withdrawn from the competition.
"The Algerians withdrew because the ladies are students and the federation says it is difficult for them to travel," Habuba added.
The North Africans could face Caf sanctions for withdrawing from the competition midway through.