Public submissions to the Turnbull government's review of religious freedom in Australia will be kept secret, in a marked departure from normal processes, according to Prime Minister Malcolm Turnbull's department.

The department, which has control of the inquiry, said it would not publish the submissions, which is in stark contrast to ordinary parliamentary inquiries, in which most submissions are automatically released.

Philip Ruddock said he wanted to be "as open as possible" in the conduct of the inquiry. Credit:Nick Moir

"Submissions to the Expert Panel will not be published online," a department spokesman said in an emailed statement. "However, where individuals provide consent, submission extracts may be included in public materials."

Late on Tuesday, however, Mr Turnbull's media team sought to intervene by suggesting inquiry chairman Philip Ruddock would decide if submissions were published. The PM's office then instructed his own department to issue a new statement to that effect.