A vacation bench of justices H L Gokhale and Ranjana Prakash Desai while passing the direction posted the matter for further hearing to June 27.
Senior counsel T S Doabia, appearing for the CGHS told the bench that the allegation of manipulation, hacking and tampering were false and unfounded.
The apex court was dealing with a petition by a girl student Pankila Mittal complaining of large-scale manipulation, hacking and tampering of the ongoing online counselling.
The bench also permitted the girl to go ahead with the process for "Diploma in Venerealogy and Dermatology" at Government Medical College Baroda, subject to the final outcome of the pending before it.
Mittal through counsel Naushad Ahmad Khan alleged that besides her, a large number of top rankers who opted for MD/MS courses, were shocked to find that due to the hacking and manipulation, they have been alloted seats in diploma courses, which is far inferior choices for their ranks.
Mittal, who secured 692 marks at the national competitive exams said she had appeared for the online counselling held on January 8 conducted by nodal agency AIIMS and had opted for as many as 24 choices in the unreserved category.
In the first round of counselling, she was alloted a seat in Seth G S Medical College, Mumbai and on May 16, she completed all formalities of admission on the basis of her rank.