In December last year, the NGT had declared the cave shrine as a "silence zone" and prohibited chanting of mantras and jayakaras beyond the entry point.
Following protests over the restriction at the cave shrine in south Kashmir, the NGT had immediately clarified that the "silence zone" rule would apply only to the area around the ice stalagmite that resembles the Shiva Linga.
The Amarnath Shrine Board had challenged the NGT order in the Supreme Court, arguing that the green court cannot pass orders on the Amarnath shrine while hearing the Vaishno Devi case, which the NGT had taken up suo motu.
The NGT based its "silence zone" order on scientific grounds that maintaining silence at the holy location would help in preventing avalanches and maintaining its pristine nature.
It called for removing iron grills in front of the Shiva Linga so that visitors could have a better view of the structure, apart from asking for a reduction of noise around the structure.
Even as the decision triggered protests last year, environment activist Gauri Maulekhi, on whose plea the NGT directions were passed, had termed it "good and progressive".
"The Amarnath cave is located in a delicate ecosystem. The directions would make the Amarnath Yatra safe and convenient for the devotees. This would protect the shrine from degradation and ensure it is protected for the coming generations," Ms Maulekhi was quoted as saying by news agency Press Trust of India.