The Morrison government's proposed anti-union laws could punish unions for past breaches of workplace laws, unions argue, potentially allowing the takeover of the militant construction union and ejection of controversial Victorian leader John Setka.

Australian Council of Trade Unions president Michele O'Neil told a Senate inquiry on Tuesday that parts of the government's Ensuring Integrity Bill were retrospective as they allowed a court to consider industrial breaches that occurred before the law commenced when disqualifying an official, deregistering a union or placing one into administration.