Clark has cited an October 2013 email between the RCMP and finance ministry as evidence the Mounties had opened a file on the health ministry probe.
The government announced serious allegations were being examined at a news conference in September 2012.
"The information that came out confirms that what the Opposition has been saying about this is absolutely not true," Clark said at an unrelated news conference at a Nanaimo, B.C. sawmill.
"The RCMP confirmed that there is an open file, and in their letter this referred to an 'investigation.'"
She added that police specifically requested the government not release all details under Freedom of Information legislation, saying their work needed to be respected.
The government heeded the RCMP's wishes, she said, adding the new email demonstrates the Opposition has "really been making things up."
"The things they've said about this are just groundless."
Eight Ministry of Health researchers were either fired or suspended in summer 2012. The government became concerned after looking into the relationship between university researchers seeking grants and employees working on B.C.'s PharmaCare program.
The affair prompted a public apology from the government for its "heavy-handed" actions some two years later, after one researcher who lost his job killed himself. Others settled lawsuits out of court.
The NDP has repeatedly called for a public inquiry, even though both Health Minister Terry Lake and Clark have offered regrets.
Opposition NDP critic Adrian Dix has charged that the government dragged the RCMP into the case, even though the government's own officials advised politicians not to mention the Mounties. He said on Thursday that Clark's new comments heighten the need for a public inquiry.
"It would all be just the usual stuff from the premier, except the consequences for these eight people were terrible," he said.
"All she can do is continue to cover up. It's disgraceful."
A government-appointed review concluded the terminations failed to follow existing procedures and reached premature conclusions. Labour lawyer Marcia McNeil concluded last December the investigation was flawed from its start.
The email prompting Clark to dismiss the NDP condemnation is dated Oct. 22, 2013. It was sent by former RCMP 'E' Division Sgt. Andrew Cowan to finance ministry official Stacy Johnson.
"To confirm, the RCMP investigation, although suspended pending the final report/investigation by your office, is not concluded," reads the email obtained by The Canadian Press. "Our file remains open with the exhibits seized from the B.C. government and Statistics Canada in our possession."
The email also says that releasing information, despite freedom of information requests, "may interfere with the investigation."
Cowan was reached in Ontario, where he was transferred in late 2013. He referred comment to RCMP headquarters in Vancouver.
Information about the case became public recently with the release of documents through a federal access to information request.
The documents outline how police tried repeatedly to obtain information that never came, and that officers eventually closed the file in July 2014.