Prime Minister Tony Abbott has been told to haul backbencher Cory Bernardi into line over what Labor says are "stupid and ignorant" comments linking burqas to the terrorism raids.

Labor Leader Bill Shorten said the comments were "out of line" and called on Mr Abbott to discipline his "rogue backbencher" for the "rampage".

Mr Abbott did not endorse Senator Bernardi's comments and stressed the raids were about crime, not religion or clothing, but he stopped short of rebuking his backbencher.

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