As India heads into a general election on Thursday, the court agreed to examine new evidence published by newspapers after it rejected the petitions last December.
The published material was privileged defence documents, the government says.
"Preliminary objections of the Centre are dismissed," said the court, led by Chief Justice Ranjan Gogoi, referring to the federal government, adding that it would set a date for further hearings.
Modi, facing a tightening election, has vehemently denied opposition allegations of wrongdoing in the purchase of 36 Rafale planes and the government had asked the court to reject the petitions, citing national security.
The arms deal has been an election issue with Modi's chief rival, Rahul Gandhi, saying it exposed the claims of his Bharatiya Janata Party (BJP)-led government's assertions of running a clean administration.
Modi indirectly admits superiority of Pakistan’s armed forces
Law Minister Ravi Shankar Prasad said Wednesday's decision was not a setback for the government and the court had only agreed to consider new evidence. "We are very sure that the review petition in the light of these facts would not be considered," he said, adding it would probably be dismissed.
Two former ministers of Modi's Bharatiya Janata Party (BJP) and an activist lawyer seeking the investigation argued that the deal's escalating price should be investigated after documents relating to some aspects were published by the Hindu newspaper.
The government told the court national security was at stake and the leak of the documents infringed the Official Secrets Act, a law dating to the colonial era.
A spokesperson for Congress, Sanjay Jha, said, "The attempt by the Modi government to stonewall the Rafale scam probe has been scuttled by the Supreme Court."
INC COMMUNIQUE
— INC Sandesh (@INCSandesh) April 10, 2019
Press release by @rssurjewala, I/C, AICC Communications, on Supreme Court decision to examine Rafale documents. #ChowkidarChorHai pic.twitter.com/NPIG2AqNkY
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