A push by the Greens and Labor to attempt to force greater protection of fisheries in Australia’s marine parks has failed for the second time.

The parties had vowed to reject controversial management plans for the parks proposed by the Turnbull government. But on Thursday the Senate crossbench combined with the Coalition to defeat disallowance motions on the basis that the parks would then be left with no plans in place and no limits on fishing.

In March the environment minister Josh Frydenberg issued management plans for 44 marine parks to replace Gillard-era plans that were suspended when the Abbott government was elected in 2013.

Frydenberg said the plans were a “more balanced and scientific evidence-based approach to ocean protection” but most environmental groups opposed them warning they would strip more than 35m hectares of “no-take” ocean from the parks, allowing commercial fishing activities in 37 of the 44 parks.

Labor introduced a disallowance motion, supported by the Greens, but it was defeated on 27 March when the government called it on for a sudden vote before the opposition had time to convince four more crossbench senators to support it.

The Greens and Labor this month proposed a series of new disallowance motions for the south-west, north, north-west, temperate east and Coral Sea marine park plans.

On Thursday the disallowance motions were defeated 36 votes to 29, with One Nation, Centre Alliance, and senators Tim Storer, Derryn Hinch, Cory Bernardi and Fraser Anning siding with the Coalition.

Greens senator Peter Whish-Wilson, the co-sponsor of the disallowances, told the Senate the choice was to “reject or reward” the government’s attempts to gut plans put in place by the fishing industry, environmental campaigners and community.

Whish-Wilson said the government had “ignored the advice of their own scientific panel” and 1,400 scientists who signed a petition urging that marine protections not be reduced.

He said claims the plans were “balanced” meant the Coalition “giving their stakeholders they represent here, the big end of the fish industry and oil and gas, what they want”.

Labor senator Louise Pratt, the co-sponsor of the disallowances, accused the government of “decimating the original plans worked on for so long by putting their vastly weakened plans forward”.

The assistant minister for agriculture and water resources minister Anne Ruston told the Senate that 2.2m square kilometres will have “no marine park protection tomorrow morning” if the disallowance succeeded.

“Your choice is clear - provide certainty for everyone who enjoys our oceans or cause more uncertainty.”

One Nation leader Pauline Hanson warned if the Greens got their way on disallowance the marine parks would “go back to no protection, nothing”.

“Why throw the baby out with the bath water? There are protections in place now and if you’re not happy with it, work on it in the next parliament.”

The Liberals and Hanson cited the Pew Charitable Trusts - the one major environmental charity that opposes the disallowance - in their reasons for backing the current marine plans.

Bodies representing recreational fishers and the commercial fishing industry welcomed the result. Seafood Industry Australia chief executive Jane Lovell said it meant the “uncertainty that has plagued much of our wild-catch sector is now gone”.

In a statement on Tuesday the Australian Marine Conservation Society warned longline tuna fisheries off the east coast are killing sea turtles in the Coral Sea.

“The Turnbull government’s decision to cut back marine protection has a shocking hidden catch - our threatened marine species are being killed in areas that would otherwise have been protected in marine parks,” said Australian Marine Conservation Society spokesman Adrian Meder.

World Wildlife Fund Australia conservation scientist Martin Taylor said the Coral Sea was one of the worst affected areas under the new plans, with more than 280,000 square kilometres of protected area downgraded.