Hearing a PIL filed by one Subodhlal Kislari on Wednesday, a division bench of justice Adarsh Kumar Goel and justice N Koteswar Singh asked the central and Assam governments to submit their probe reports within a month.
The PIL also held Ajmal responsible for the Azad Maidan violence in Mumbai in August.
Ajmal welcomed the court directive. "I am not worried because I was in no way involved in the violence," he said from New Delhi.
The All Bodo Students' Union said the court directive was timely. It, however, said Ajmal's 'inflammatory' press conference in Delhi a few days ago should be brought within the probe ambit.
"Ajmal had told the media in Delhi that Bodos ran bulldozers over Muslims, which provoked Muslims elsewhere," union president Pramode Boro said.
The court order coincided with the bail granted to Bodoland People's Front (BPF) legislator Pradeep Brahma, in all the seven cases filed against him for instigating the ethnic violence.
BPF, a partner of the Congress in the ruling coalition, runs the Bodoland Territorial Council (BTC) where the violence had taken place since July 20.
Meanwhile, BTC chief Hagrama Mohilary has threatened to boycott the process of rehabilitating the victims of violence after the CBI raided the offices of the BPF's youth wing.