Rafiq Jutt from Gujarat was arrested in 2008 and tried under Section 59 of the Pakistan Army Act, which allows the military to try civilians for spying.
The Islamabad High Court (IHC) took up the petition filed by the Indian High Commission yesterday but it was returned due to technical objections raised by the registrar.
A court official said that the registrar's office said that power of attorney was not properly signed. It also objected that respondents were not clearly named in the petition.
Advocate Malik Shahnawaz Noon, the petitioner's counsel, told the media that he would re-file the petition after removing the anomalies pointed out by the registrar.
The petition sought the release of Mr Jutt as he completed his sentence, according to Mr Noon.
He said that Mr Jutt was visiting Pakistan on a valid visa when he was arrested.
Mr Jutt was kept in different jails during his sentence period. Presently, he is lodged in Central Jail Karachi, Mr Noon said.