Hearing the PIL filed by Kolkata-based NGO India's Smile, Chief Justice Arun Mishra said the special division bench would be constituted by acting Chief Justice Asim Banerjee to look into the matter.
Justice Joymalya Bagchi, who was part of the division bench which heard the case today, said since he was involved in the Mukherjee Commission which had investigated into the case once, he would not take up the matter.
The petition demands declassification of all documents, including top-secret files, relating to Netaji so that the mystery surrounding his disappearance could be solved.
The Prime Minister's Office had earlier refused to furnish data on documents and records it held on Netaji's disappearance, saying the disclosure would harm India's relation with foreign countries.
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The petition demands a judicial review on whether the documents should remain secret in public interest.
When under house arrest by the British colonial administration, Netaji had escaped from India in 1941 to seek international support for freedom struggle. After organising the Indian National Army with Japanese help he went missing in 1945.
He was last seen at the Bangkok Airport on August 17 1945. The Mukherjee Commission had rejected the opinion that he died in a plane crash in Taiwan on August 18, 1945.