The NSW lower house voted on Friday afternoon to send the parliamentary budget bill straight to the state's governor for royal assent -- without the funding boost agreed on by the upper house.

It is the first time in more than 20 years the parliament has referred a law to the governor disregarding changes made by the upper house.

Under an amendment to the bill introduced by the Greens in the Legislative Council on Tuesday, the Independent Commission Against Corruption would get an extra $7.3 million in funding for 2020/21. All non-government parties supported the amendment.

But the government says the upper house does not have the power to amend the parliament's budget.

Treasurer Dominic Perrottet moved in the Legislative Assembly on Friday to send the Appropriation (Parliament) Bill to Governor Margaret Beazley to be signed into law, without the upper house amendments.

Mr Perrottet invoked a rarely used part of the state's constitution when moving the motion.

He proffered two opinions from the state's solicitor-general in support of his move, one from 2020 and one from 1992. Neither advice considers this bill specifically.

"The Greens and One Nation do not write the budget, the government does," Mr Perrottet said, adding that they should "learn their place".

Speaker Jonathan O'Dea acknowledged the issue was "unsettled" and said he would leave it for the Legislative Assembly to decide what to do.

However, he rejected a point of order seeking to rule out Mr Perrottet's motion because the advices did not support the opposition's position.

Opposition Leader Jodi McKay said she was "shocked and very concerned" that the government would not agree to the additional funding for ICAC, which is said to bring its funding in line with inflation increases.

It was "extraordinary and unprecedented" that the government would seek to refer a bill to the governor without upper house changes, she said.

"They are ignoring the will of the upper house which passed this amendment with significant support and that is how the parliament should work," Ms McKay said.

Labor and the Greens want ICAC's funding model to be determined independently, arguing that it has been starved of the funds it needs to run complex investigations. Currently, a cabinet committee signs off on its funding requests.

Ms McKay on Friday referred to Premier Gladys Berejiklian's recent appearance before ICAC, where she admitted to having a long-running, secret affair with Liberal MP Daryl Maguire, who was being investigated by the watchdog.

"For the premier to cut additional funding presents itself a major issue and a conflict of interest," Ms McKay said. Ms Berejiklian was not in the chamber.

ICAC told a parliamentary inquiry last year that its annual funding had been below inflation for most of the 30 years since its inception, leaving it with a $7.2 million budget shortfall.

Last month, an auditor-general report said the current funding model threatens ICAC's independence, given funding decisions are made by people who might be subject to investigations.

Australian Associated Press