The Coalition had expected its bill to crack down on rogue unions to pass, after intense negotiations with Senate crossbenchers.

But Senators Pauline Hanson and Malcolm Roberts stunned the Senate by voting it down.

Since the 5pm vote, her office had been inundated with calls, she said.

"We have got people actually crying on the phone thanking us. That's how the Australian workers out there feel about this, they feel relieved about this bill going down. And if I've done that to give people hope that someone really cares and thinks about them, then it's been worth it."

One Nation's feint appeared to stun the Coalition, and its Senate leader, Mathias Cormann.

On Wednesday, it appeared One Nation would support the government, after Senator Roberts said while the party could not support "union bashing", nor a bill that deregistered organisations for "misdemeanour offences like not getting their paperwork in on time", it had negotiated protections.

But Senator Hanson said "a lot of things have actually eventuated this week that enshrined how we would vote".

The pair had spoken about it on Thursday and made a final decision, she said, confirming she had given the government and her fellow crossbenchers no warning.

While the government said it would bring the bill back "at the appropriate time", One Nation didn't identify specific changes that would win its vote, saying broadly that it wanted "action on white collar crime".

The government has Rex Patrick and Stirling Griff on board after negotiating amendments with the pair, but without One Nation can only look to independent Jacqui Lambie for the final vote, if it decides to try again.

Senator Lambie had set out amendments that would win her support, but the government rejected them this week, focusing on One Nation.

Senator Lambie was left angry.

"They were too cocky that they'd get their win without me. Well, guess what. Look where that gets you," she said.

"I gave the government the chance to support amendments that protect good unionists and line up bad ones. They said no, we'll go it alone, and they lost. Now there's nothing. And thanks to the Coalition's bloody-minded arrogance, they have nothing to show for their work."

The bill suggested teachers, nurses and firies were "as bad as the CFMEU", she said.

"It puts the bloody Musicians' Union of Australia in the same camp as the ETU for goodness sake! There's no need to put everyone in the firing line."

Attorney-General Christian Porter said he was "very disappointed in the result".

The government remained committed to the bill and would bring it back, he said.

"It's for Pauline Hanson to explain why she voted against a bill that met every requirement she sought through extensive consultation," Mr Porter said in a statement.

"This is important reform which seeks to ensure that registered organisations obey the law. It is as simple as that."

The legislation would have enabled unions to be deregistered off the back of serious criminal breaches.

Australian Council of Trade Unions secretary Sally McManus said the Senate vote was a rejection of "double standards".

"Never underestimate working people," Ms McManus said.

Senator Hanson said the bill would have given "unfettered powers" to administrators appointed over unions.

"Once appointed, administrators could perform any function, or exercise any power that the organisation or its officers can perform," she said.

"We have seen the highly questionable behaviour of administrators, liquidators, receivers, and managers exercise unlimited powers on their appointment by the banks.

"Under no circumstance was I going to unleash their unlimited power and zero accountability on Australian unions or other registered organisations."

Workers were worried about foreign workers, free-trade agreements, wages and conditions, she said.

The bill had been directed at the CFMMEU but the government should not go after one organisation without cleaning up bullying, thuggery and corruption also in white collar jobs.

But union bosses should consider the events "a warning shot across the bows to ... get their act together".

The loss capped off a disastrous week for the Morrison government, which has been fending off sustained attacks on Energy Minister Angus Taylor over the doctored document scandal.

Prime Minister Scott Morrison found himself in the firing line over a call he made to NSW Police Commissioner about a strike force set up to investigate the origin of the fake travel figures Mr Taylor used in his letter to Sydney Lord Mayor Clover Moore.

NSW Greens MP David Shoebridge has now referred Commissioner Fuller to the Law Enforcement Conduct Commission over the matter.