Justice Manmohan dismissed the plea terming it "premature" and said the police has already been investigating the issue.
"The incident took place only on February 9. This court is confident that Delhi Police will investigate all the aspects. The petitioner approached the court without making any representation to any government authorities. The petition is premature," said the court.
"I am not interfering at this stage. Let the Delhi Police investigate it. Its too early. Incident took place on February 9 only," the court said dismissing the plea.
Centre's counsel Anil Soni and Delhi Police's counsel Rahul Mehra told the court that anti-national slogans were shouted in the campus and police is investigating who instigated it and who were behind it.
The plea sought National Investigation Agency (NIA) probe and judicial inquiry into the alleged anti-national activities at the JNU here.
Advocate Ranjana Agnihotri also sought the appointment of a judicial commission to look into the February 9 incidents on the JNU campus.
Jawaharlal Nehru University Students Union president Kanhaiya Kumar was arrested in a sedition case on February 12 after an event held on the university campus against hanging of parliament attack convict Afzal Guru.
On February 12, Kumar was remanded to a three-day police custody by a court here. On Monday, his police custody was extended by two days.