Ngcongca injured the posterior cruciate ligament in his knee late last month in a Uefa Europa League clash against FC Luzern, ruling him out of South Africa's internationals against Brazil and Mozambique.
His non-arrival in Brazil raised the ire of coach Gordon Igesund, who claimed he was not informed of the injury and had waited patiently in Sao Paulo for the fullback to arrive.
Siboniso Gaxa was called up in Ngcongca's place, but the Kaizer Chiefs man has subsequently been ruled out for the next four to six weeks himself.
Ngcongca's return ahead of the internationals against Poland and Kenya next month would be well-timed for Igesund, but whether the player will be fully fit for those games remains to be seen.
"Anele got the green light from the medical staff to start kicking the ball and (in part) to resume training with the squad," Genk said. "When he will regain full fitness will depend on how he responds to training."
Ngcongca is a highly-prized member of the Genk squad and had been operating as a centre-back earlier in the campaign, to cover for injured teammates.