About 30 people protesting against offshore processing were removed from the chamber at the beginning of Question Time.
Several had glued their hands to the railing, leading to suspension of proceedings for half an hour.
The Speaker has promised a full investigation.
"Every aspect of today's occurrence will be investigated and I will report back to the house on the matter."
It was soon back to business as usual, with the government keen to talk up its success on passing legislation for the Australian Building and Construction Commission through the senate.
The issue had been a double dissolution trigger for July's federal election.
Earlier in the day, the Prime Minister described its passage as a victory for Australian families.
"We are restoring the rule of law to the construction sector. This is a great day for Australian families. This is not union-busting. This is economy-boosting. This is job-boosting. This is small business-boosting. It is backing the rule of law, it is backing Australians to get ahead, and I am proud to lead a government that is delivering on the commitments it took to the Australian people in the election."
The bill was passed with a raft of amendments demanded by the crossbenchers.
One Nation, the Nick Xenophon Team, Derryn Hinch and David Leyonhjelm supported the Coalition, while Jacqui Lambie voted with the Greens and Labor.
As sweeteners, the government added extra oversight for the commission's coercive powers, a requirement for building work to be offered to locals, security of payments for subcontractors, judicial review and a review within a year.
Senator Derryn Hinch denies selling out his principles to support the bill.
"I said when I got here, compromise is a word that I'm not used to but I'm starting to work out it can work, and unlike some of the crossbenchers, I can look you in the eye and say, 'I made no deal,' there was no horse-trading, I just said, 'this is where I stand, this is what I think is fair' and this is where we've got to."
The Greens accused independent Senator Nick Xenophon of failing to deliver on his promises over water entitlements from the Murray-Darling Basin.
Senator Xenophon had threatened to hold up the ABCC legislation until the government found an extra 450 gigalitres of water to restore the health of the Murray River.
However, he dropped his demand after Prime Minister Malcolm Turnbull wrote to South Australian Premier Jay Weatherill outlining a plan to strengthen scrutiny of the basin plan.
Senator Hanson-Young says Senator Xenophon has disappointed South Australians.
"We know that 450 gigalitres must be guaranteed for it to get into the system, Barnaby Joyce, the National Party, working very hard to ensure that gets dumped. Here we have Nick Xenophon in the most powerful position, squibbing it right at the very end. I don't think South Australians will be particularly happy. It's one thing to promise you can deliver things, it's another thing to follow through with it."
Senator Xenophon says the criticism is unfair.
"When the Rudd government was in power, in 2009 I negotiated a package of measures for the biggest water buybacks of $500 million in one hit, $200 million for River Murray communities, and $200 million for stormwater harvesting as well as an additional package for distressed irrigators to help them out."
Employment Minister Michaelia Cash, who guided the legislation through the Senate, dismissed criticism that the amendments weaken the ABCC.
"This is an important win for the Australian people. This is all about cultural change within the building and construction sector. When the bill receives royal assent, which I hope will be as soon as tomorrow, that cultural change starts."
However, any vindication the government may have felt was soon tempered by its failure to pass its proposed 15 per cent rate on the backpacker tax.
Senators Derryn Hinch and One Nation's Rod Culleton voted with Labor, the Greens and crossbenchers Jacqui Lambie and David Leyonhjelm on a rate of 10.5 per cent.
