"One country of itself deciding it's time to withdraw isn't all that significant," Senator Hill said at a news conference.
"(But) what we don't want to see is that this becomes a trend," he said.
Mr Howard on Monday condemned a decision by Spain's incoming Prime Minister, Jose Luiz Rodriguez Zapatero, to withdraw 1300 troops, saying it would only lead to further bloodshed in Iraq and encourage insurgents.
Labor's foreign affairs spokesman, Kevin Rudd, seized on the apparent contradiction, saying Senator Hill's comments had undermined the Prime Minister.
"There is now a fundamental split within (the) Government over its position on Iraq," Mr Rudd said.
"John Howard says Spain's withdrawal is the end of the world and Senator Hill says its not significant," he said.
"This Government's all over the place on Iraq."
In another development radical Shi'ite cleric Moqtadr al-Sadr has told Australian troops to leave Iraq, warning they will be kidnap targets for as long as they "occupy" the country.
Mr Howard dismissed the cleric's threat.
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