Le Journal de Montreal reporter Eric-Yvan Lemay, who has not been charged, was with his pregnant wife and two young children when police banged on the door at 6:45 a.m. to serve a search warrant.
The newspaper's managing editor, George Kalogerakis, says police demanded Lemay's fingerprints, some clothes and his computer.
Kalogerakis says the seized material was sealed until Le Journal contests the warrant in court.
Kalogerakis said Lemay had recently done a series of articles on how easy it was to get medical information in about 10 hospitals, including one in St-Hyacinthe where he found a stack of medical records in a corridor.
He says one of the hospitals reportedly filed a criminal complaint against Lemay.
Lemay has not been charged but Kalogerakis says he is suspected of theft under $5,000.
Le Journal reported he is suspected of trafficking in confidential documents.
Lemay, who is also an assistant editor at the newspaper, was looking at the lack of privacy for patients in hospitals.
Kalogerakis says when Lemay found the stacks of documents in the St-Hyacinthe hospital he videotaped himself opening and closing the files.
"He didn't take them out of the hospital," Kalogerakis said. "He did not at any point take anything out of the hospital."
Names of the patients were blacked out when the newspaper published the video on its website.
"Our job is to ensure that the interests of our readers and the public are defended," Kalogerakis said.
"We consider what we did was in the public interest to show there is a problem with how the health system is dealing with confidential medical records."
He described the incident as a case of "shooting the messenger."
Kalogerakis said the day after the stories were published the health minister told hospital adminstrators to do a better job of protecting information.
No date has been set for the challenge of the warrant in court.
The Canadian Association of Journalists said it was deeply concerned to hear about the police raid.
"The CAJ cannot understand at this time why the journalist who exposed the hospitals' apparent inability to lock down confidential patient information has become the subject of a criminal investigation," association president Hugo Rodrigues said in a statement.
"It's mind-boggling the province has chosen to investigate the messenger rather than show itself taking action on protecting patient confidentiality."