"Subhash Shirodkar who runs this college where these skeletons were found should be investigated," Parrikar, who also holds Home portfolio, told members of BJP state executive here.
Nine skeletons were found in the backyard of Shree Kamaxi Homoeopathic College in Shiroda village last weekend.
"First we need to find out whether these skeletons are of men or women," the chief minister said, adding that recovery of human remains was a serious matter.
'Serial killer' Naik allegedly killed 18 women and is currently facing trials in various courts in the state.
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Incidentally, Naik also hails from Shiroda village.
Parrikar questioned the "silence" maintained by Opposition Congress on the incident.
"If these skeletons were found anywhere in Panaji (Parrikar's constituency), Congress would have made an issue out of it," he said.
When contacted, Shirodkar told PTI that he was ready to face any investigation.
"I am ready for any investigation. These cadavers were brought for study purpose in the college. We have the records to show that these remains were buried in the pit after securing due certification from state pollution control board.