Speaker Vicki Dunne held a church service on Monday to mark the start of the parliamentary year.
All eight Labor MLAs and Greens MLA Shane Rattenbury boycotted the service, saying the assembly should remain a secular institution.
"This is an assembly for all Canberrans, it should be separate from the practice of any particular religious faith," he said.
Chief Minister Katy Gallagher says it is an important change.
"It is important that that secular history and tradition be maintained," she said.
But the Liberal Party labelled the motion offensive.