Queenslander Susan McDonald crossed the floor on Thursday to support scrapping regulations affecting Angel Flight, a charity that co-ordinates flights to attend medical appointments.

The Civil Aviation Safety Authority put additional maintenance requirements imposed on the flights in response to two deadly crashes in 2017 and 2011.

Senator McDonald chaired a parliamentary inquiry that found there was no link between maintenance and the triple-fatality crashes in Victoria and South Australia.

Centre Alliance's Rex Patrick was behind the disallowance motion, which was shot down 29 votes to 12 after the government and opposition opposed it.

As Labor frontbencher Louise Pratt confirmed her party would not support the motion, Senator Patrick shouted "Because you're cowards" across the chamber.

Senior cabinet minister Simon Birmingham said the government supported the independence of CASA.

"These measures are a practical approach to mitigating any flight risks," he told parliament on Thursday.

He said CASA's advice was appropriate and proportionate, with the regulation expected to affect less than 10 per cent of private aircraft.

Senator Patrick said Australian Transport Safety Bureau's finding that Angel Flights were seven times riskier than private aviation had caused a significant rise in the organisation's insurance premium.

He echoed the criticism in the parliamentary committee's bipartisan report which raised concerns with the ATSB's research.

"Lies, damned lies and statistics is the saying," the SA senator said.

Senators Patrick and McDonald warned costs for Angel Flight would be driven up.

"CASA's approach risks driving pilots out of the Angel Flight service which is so critical to Australians living in rural and remote areas," Senator McDonald said.

She said people with chronic illnesses would be faced with driving hours or being stung by high airfare costs to attend appointments.

"It is painfully apparent that CASA imposes regulation simply for the sake of it," the first-term Nationals senator said.

Senator Patrick said CASA chief executive Shane Carmody's tenure must be reconsidered.

Liberal senator Hollie Hughes also praised Angel Flight, which helped transport her autistic son from Moree in rural NSW to medical appointments.

"Angel Flight was an absolute godsend for our family," she said.

"That (CASA) are trying to take away a service that provides a vital lifeline for families is just absolutely incomprehensible."

Australian Associated Press