The court directed the Central Bureau of Investigation to probe the alleged role of Jagdish Tytler, a month after a case against him was closed.
However, a witness said recently he saw Mr Tytler lead a mob against Sikhs.
The riots, sparked by the assassination of PM Indira Gandhi by Sikh bodyguards, left more than 3,000 Sikhs dead.
Mr Tytler is a MP with the ruling Congress party, and has consistently denied any role in the rioting.
'No evidence'
In November, the Central Bureau of Investigation (CBI), India's top central detective agency, closed a case against Mr Tytler saying there was "no evidence" or "witness" to establish that he had a role in the rioting.
However, Jasbir Singh, who lives in California, recently claimed that he saw Mr Tytler lead a mob on a Sikh temple in Delhi during the riots.
Three Sikhs were burnt to death in the attack on the temple.
Mr Singh, who lost 26 family members in the rioting, left the country after the incident.
Now the court has asked the CBI to carry out a fresh investigation into Mr Tytler's alleged role and submit a report by 16 January.
Mr Tytler was earlier implicated by a judicial commission set up to investigate the 1984 killings.
The report, by retired Supreme Court judge GT Nanavati, was the ninth inquiry commission into the riots, and was set up in 2000 by the then governing Bharatiya Janata Party (BJP) which is now in opposition.
The inquiry found "credible evidence" against Mr Tytler and recommended further investigation into his role.
Mr Tytler submitted his resignation as a minister for expatriate Indians after being implicated in the riots.
He said he had resigned to have his "name cleared".
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