The deal also involved Kuala Lumpur-based business tycoon T Ananda Krishnan.
The NGO, Centre for Public Interest Litigation and Janata Party President Subramanian Swamy, had filed applications in the apex court alleging that Foreign Investment Promotion Board (FIPB) approval to the Aircel-Maxis deal was granted fraudulently.
"Investigation with reference to subject matter of your application has made some progress, but there are some difficulties," a bench comprising justices G S Singhvi and K S Radhakrishnan told Swamy.
Senior advocate K K Venugopal, appearing for the CBI, had placed before the bench in a sealed cover the progress reports of the probe by the CBI and Enforcement Directorate.
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The bench in its order noted that the CBI report also dealt with its probe into the alleged violation by FIPB in the Aircel-Maxis deal.
Venugopal told the bench that a CBI team had met with the Attorney General of Malaysia on March 21 and there was a detailed discussion based on the letters rogatory (LRs) sent to Kuala Lumpur.
However, he said Malaysian authorities are going through the materials on the issue to ascertain whether there was any element of criminality involved in the deal or not.
At this, the bench wanted to know what would be the situation if the Malaysian authority declined assistance in the probe.
Venugopal said in such case "we have to make out a prima facie case based on our investigation here".