The security measures around Australia's controversial e-health records system will be examined in a parliamentary inquiry.

My Health Record came under fire when it was due to be fully rolled out over concerns people's data would not be protected adequately.

The government on Wednesday supported the Greens' reference to the Senate's community affairs committee - identical to one proposed by Labor for another committee - which will look at privacy concerns and other issues with the system.

The decision to switch My Health Record from opt-out to opt-in will come under the microscope, as will third-party access to data.

Health Minister Greg Hunt has promised to change laws so police and government agencies will need a court order to obtain patient data.

Greens leader and doctor Richard Di Natale said there were serious concerns around the My Health Record system.

"The government has shown itself to be incapable of protecting the privacy of citizens on a range of issues," Senator Di Natale said.

Liberal frontbencher James McGrath said the committee would show the benefits for patients and doctors.

"This reference will also provide an opportunity to address any misconceptions or concerns about the My Health Record system," Senator McGrath said.

The system was released for national public access last month after a six-year trial, with legal experts since warning of a loophole that could put family violence victims at risk.