Labor's Deputy Senate leader Kristina Keneally has infuriated the Government and annoyed some of her ALP colleagues by breaking a bipartisan agreement on terrorism legislation — and then boasting about it.

Key points: The Crimes Legislation Amendment Act gives police the power to stop and question people in airports

The Crimes Legislation Amendment Act gives police the power to stop and question people in airports Labor had advised the Government it would support a Centre Alliance amendment for a review of the bill but indicated it did not support a sunset clause

Labor had advised the Government it would support a Centre Alliance amendment for a review of the bill but indicated it did not support a sunset clause Senator Keneally said Labor had decided during debate on the bill to "test" the will of the Senate

The ABC understands that the chair of the Parliamentary Joint Committee on Intelligence and Security (PJCIS), Liberal MP and former SAS captain Andrew Hastie, took Senator Keneally to task for diverting from an agreement to fully support bipartisan anti-terrorism laws.

The Crimes Legislation Amendment (Police Powers at Airports) Act gives police the power to stop and question people in airports who they believe are acting suspiciously.

It also allows police to bar people from the vicinity of airports for 24 hours.

The legislation was developed in response to a foiled Islamic State plot to blow up a 2017 Etihad Airlines flight from Sydney to Abu Dhabi.

Labor and the Coalition had agreed to support the bill's passage, but last-minute manoeuvring on Monday night saw Labor support a four-year sunset clause to the laws, drafted by Centre Alliance's Rex Patrick.

The amendment's passage was aided by the fact that South Australian crossbencher Cory Bernardi had left Parliament unwell and had not been given a "pair" to cancel out the effect of his absence.

Earlier that day, Labor had advised the Government it would support a Centre Alliance amendment for a review of the Police Powers bill but indicated it did not support a sunset clause. Labor argues this indication was not binding.

But at 8.42pm on Monday night, Senator Keneally tweeted that the Government had "just lost a vote in the Senate".

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"We successfully amended the Police Powers at Airports Bill to include a PJCIS review of the legislation & sunset clauses as safeguards," her tweet said.

"As @ScottMorrisonMP says such matters "can't be set & forget" -- now they won't be #auspol."

The Government is furious at Labor's Senate antics and some of Senator Keneally's Labor colleagues are similarly unimpressed.

Mr Hastie raised the matter with Senator Keneally when the PJCIS met on Thursday morning in the super-secure briefing room, which is adjacent to the cabinet room.

It is understood Senator Keneally was politely reminded of the strength derived from the bipartisan nature of the powerful intelligence and security committee.

Senator Keneally told the ABC that Labor had decided during debate on the bill to "test" the will of the Senate.

"During the debate on the amendments, the Government did not vote against Centre Alliance's recommendation for a review of the Police Powers bill and allowed it to pass," she said.

"This is contrary to what the Government indicated to Labor earlier in the day, when they said they would vote to oppose both Centre Alliance amendments.

"Given the Government did not vote to oppose Centre Alliance's first amendment to hold a review of the bill, Labor decided to test the will of the Senate on a sunset. Labor supported the Government's Police Powers bill and it passed the Senate."

Home Affairs Minister Peter Dutton said Senator Keneally's "unilateral decisions" were "completely at odds with the leadership of the Labor Party".

"Kristina Keneally, honestly, is off the reservation," Mr Dutton said.

"People in Labor are distancing themselves from her. Richard Marles has completely distanced himself from her, as has Penny Wong."

Senator Keneally said what worked well with the PJCIS is that "we have robust policy debates but emerge with a bipartisan and considered approach to protecting the national interest".

"It's a committee unlike any other in the Parliament, and I pay tribute to Andrew Hastie who, as chair, does a good job landing our reports with the full support of all members," she said.

"It is the case, however, that sometimes the Cabinet process results in PJCIS recommendations not being adopted. For example, the encryption bill and the Temporary Exclusion Order legislation both proceeded with the Liberal Government deciding not to adopt the bipartisan recommendations of the PJCIS.

"In both cases, Labor nonetheless supported the Government's bills in the interest of national security."