While the hijacking was condemnable, any attempt to prosecute the two, who had already completed life terms in Pakistan for the crime, would amount to a serious travesty of justice, he said in a statement, adding that this could tantamount to "double jeopardy".
He said he has directed the legal aid team of the home department to extend legal help to the two, if required.
Saying he did not want to go into the merits of the case since it was sub-judice, Mr Singh pointed out that 36 years was a long time, especially considering that their life term would not have been more than 14 years.
The Srinagar-bound Indian Airlines plane with 107 passengers and six crew members was hijacked and taken to Lahore in September, 1981.
The main hijackers namely Gajender Singh, Karan Singh, Satnam Singh, Jasbir Singh and Tejinder Pal Singh had demanded the release of Sikh preacher and head of Damdami Taksal Jarnail Singh Bhindrawale who was arrested on September 20 the same year in a murder case.
Later, Bhindrawale was killed during Operation Blue Star in 1984.
Hijackers were arrested in Lahore, Pakistan and were convicted and sentenced to life by the special court there.
After completing the sentence, Satnam Singh returned to India through Nepal in 1999 and surrendered before the trial court in New Delhi. The court released him on bail and in 2002, he was discharged on the ground of double jeopardy.
Tejinder, who returned to India in 2000, also filed his application for discharge before the Additional Chief Metropolitan Magistrate, Delhi on the same ground but the court said it was not bound by the order of preceding court and dismissed the application. The other three accused are still abroad.
Satnam and Tejinder are now facing sedition charges in India, which their counsel has described as a "classic example of double jeopardy", as the duo's entire life would be spent in facing one trial after the other for the "same set of facts".