Tasmania's Lower House has passed a bill to remove abortion from the criminal code after a marathon debate.

MPs were granted a conscience vote on Health Minister Michelle O'Byrne's private member's bill.

It removes abortion from the criminal code and allows terminations at up to 16 weeks.

But the speaker Michael Polley was alone in crossing the floor after a debate that stretched into the early hours of this morning.

Attorney-General Brian Wightman said supporting the bill was the toughest decision of his political career.

"It is not my right to dictate to women how, and in which circumstances, they should be made to lose control of their own bodies," he said.

All Opposition MPs voted against the bill, including health spokesman Jeremy Rockliff who told parliament he was pro-choice.

"I believe a change is needed in this area and I'm committed to pursue it, but equally I'm committed to ensure it is acted upon to the rigour of proper process," he said.

Braddon Liberal Adam Brooks also voted against the bill despite being pro-choice.

The bill will now be considered by Upper House where it is likely to face tougher scrutiny.