A bench of Acting Chief Justice Gita Mittal and Justice C Hari Shankar said that though it agreed with the petitioner's view, but it cannot grant the relief sought.
"Though we agree with the petitioner that 'Vande Mataram' be recognised by the respondent as equal to 'Jana Gana Mana'.
We are of the view that we are unable to grant the relief sought in the petition," the bench said.
The court's order came on a plea of Delhi resident Gautam R Morarka, who had urged the bench that directions be given to the Centre in this regard so that proper dignity and respect can be maintained when 'Vande Mataram' is played or sung.
The Centre had opposed the plea saying 'Vande Mataram' occupies a "unique and special place" in the psyche of Indians but it cannot be treated at par with 'Jana Gana Mana', penned by Nobel laureate Rabindranath Tagore.
Seeking dismissal of the PIL, the Ministry of Home Affairs (MHA) had said the plea that 'Vande Mataram' be treated on par with 'Jana Gana Mana' cannot be accepted.
The PIL had also sought a direction to amend the 1971 National Honour Act accordingly to ensure equal respect for 'Vande Mataram'.
The MHA had said that on the petitioner's representation and subsequent PIL, it had set up a committee which had met on March 29, 2016 and recommended that status quo be maintained in this regard.
The panel had expressed hope that every citizen would remember the historic role of 'Vande Mataram' in the freedom struggle and show due respect to it whenever it is played or sung, it had said.
"It has become synonymous with valour, dedication and love for one's motherland and does not require any crutches to hold it (the song) in the heads and hearts of India's citizenry," the MHA had said.
Mr Morarka in his plea had said even in 1950, the then President of India had said that 'Vande Mataram' shall be honoured equally with 'Jana Gana Mana'.