The Christian prayer has opened each day of parliament for more than a century, as part of a tradition inherited from the British during colonial rule.

But Harry Jenkins, speaker of the house, has questioned the relevance of the prayer in an increasingly secular and religiously diverse nation.

He said MPs and members of the public had repeatedly raised the issue with him since he took office in February.

"One of the most controversial aspects of the parliamentary day ... is the prayer," he told the Herald-Sun newspaper. "On the one end of the spectrum is: Why have a prayer?" Mr Jenkins said an indigenous recognition would be in line with Prime Minister Kevin Rudd's historic apology to Aboriginal Australians in January for injustices suffered during 220 years of white settlement.