The division bench headed by Justice V K Tahilramani was hearing a petition filed by Shetty's brother Sandeep Shetty, which alleges irregularities in the CBI probe and seeks prosecution of a former CBI Director and a special director.
S P Singh, the investigating officer, was pressurised by superiors to file a closure report in the case, it alleges.
CBI's lawyer Hiten Venegaonkar today informed the court that the present CBI Director had decided that the case will be re-investigated and the probe will be carried out by CBI Delhi's special crime branch instead of its Pune branch.
His petition states that till February 2014, the CBI investigating officer maintained they were on the right track, but later he seemed to be under "tremendous pressure" and someone was "jeopardising the probe".
Shetty was stabbed to death near his house on January 13, 2010. The case was transfered to CBI on April 6, 2010 after Sandeep Shetty had moved the HC.