A bench of Justice Madan B. Lokur and Justice Deepak Gupta sought their response in four weeks and posted the matter for hearing in August.
The Central government told the bench that the scheme for rehabilitation had been finalised and was to be taken up by the state cabinet for its approval.
Since there is no elected government in the state, the plan is now stalled, added counsel appearing for the Centre.
The bench, after going through the photographs of blackened water of the BanGanga, a tributary, near the Vaishno Devi Shrine, due to dumping of animal dung and human waste, said it is a "serious problem".
During the hearing, the petitioner, activist Gauri Maulekhi, alleged that the Vaishno Devi Shrine Board has not done anything to limit the pollution caused by large number of mules or the unsustainable number of pilgrims as it "makes money".
The Nation Green Tribunal (NGT) had earlier said new path should be created to the shrine exclusively for pedestrians and battery-operated cars and directed that no horses or mules would be allowed on the new route to the shrine.
The apex court was hearing the plea filed by Maulekhi, who had earlier filed a plea in the NGT seeking removal of horses and mules from the path to the shrine, saying there were two issues -- one about environment and pollution there and the other on opening of the new track for battery-operated vehicles.
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