Staying the announcement of the awards till July, Justice Kailash Gambhir directed the union information and broadcasting ministry to examine the allegations levelled by jury member Sahyamli Banerjee Dev in a petition that the awards were "fixed".
"It is serious as the dissent is by a jury member," said Justice Gambhir.
Restraining the ministry from declaring the awards without court's prior permission, he also directed it to submit to the court the decision taken by the jury on selection of films for the awards.
The judge also sought the government's action taken report on the allegations in the petition by Deb before the court by next date of hearing on July 26.
In her petition, Dev has alleged that Sanjay Leela Bansali's "Black" doesn't qualify for the best film award and is an adaptation of the English feature film "The Miracle Worker" of 1962.
"A film which is an adaptation of a foreign film should not be considered since the awards are meant only for original works," said Deb in her petition.
During the arguments Dev's counsel Deepak Prakash alleged that the two officials of the Directorate of Film Festivals (DFF), Shanker Mohan and Manoj Srivastava, had suggested the names of the awardees to Jury Board Chairman B. Sarija Devi during a meeting held at Ashoka Hotel in New Delhi on August 12, 2006.
"Those who have close proximity with the DFF officials were up on the bid for the National Awards while a number of promising directors were left out because they did not manage to build up connection with the authorities," said the petition by Dev.
"In reality the DFF officials with ulterior motives decided the awards in their chambers and constituted a jury for the name's sake and then they tried to influence the members of the jury," the petitioner said.
Citing an example of irregularity in the selection process of the award, the petition said that Tamil films `Anniyan' and `Apaharan' had been rejected in the preliminary round, but chosen respectively for the best special effect and the best screenplay awards.
Deb said in her petition that Rahul Dholakia should not have been chosen for the best director's award for the film 'Parzania' as the film did not bear his signature as an author or director.
She said she had made two representations to the ministry expressing her dissent on the selection of the awards, but the authorities did not bother to reply.
The information and broadcasting (I&B) ministry officials had earlier said that with the Supreme Court vacating the stay on the awards last month, the list of the winners was likely to be released by May 12.
The awards had been kept in abeyance, following a Bombay High Court order, directing the directorate of the film festivals to consider uncensored films for the competition.
The dispute started when the directorate did not take into account the high court order and refused to consider uncensored films for the competition.