Conservationists are outraged over the Federal Government's draft plans for 44 Australian marine parks, saying it almost halves the protections set five years ago.

Under the new proposal, mid-water trawling will be allowed and more areas will be opened to commercial and recreational fishing.

Marine park zones: Category 2012 2017 Green (high level protection) 36% 20% Yellow: (allows for sustainable use, but protects seafloor) 24% 43% Blue: (allows for sustainable use) 40% 37% Source: Parks Australia

Green zones, which offer the highest protection, will be reduced but yellow zones, which allow for sustainable use but protect the seafloor, will be increased.

The plans cover Commonwealth waters off the coast of New South Wales, Queensland, Western Australia, South Australia and the Northern Territory starting about five kilometres offshore.

In 2012, the then-Gillard government expanded the network of marine reserves but they were suspended from operation under then-prime minister Tony Abbott, who ordered an independent review.

The new draft plan, aimed at striking a balance between commercial fishing operations and protecting the environment, was released in July.

Removal of Geographe Bay protection 'inexplicable'

No-take fishing zones set up to limit fishing in Geographe Bay off the West Australian coast have been scrapped under the new plan.

About 30,000 humpback whales move down the WA coast to migrate, proving a major drawcard for tourists

The new plan scraps no-take fishing zones in WA's Geographe Bay. ( ABC News: Louisa Rebgetz )

Marine campaigner Adrian Meder has worked along the south-west WA coast for 20 years and described the plans as a "bit of a clanger".

"It's sort of inexplicable that the Government would propose getting rid of the most meaningful protection in our bay," Mr Meder said.

Environmentalist Michelle Grady from Pew Charitable Trusts echoed the concerns.

The Federal Government's draft plan affects 44 Australian marine parks. ( ABC News: Louisa Rebgetz )

"We're very surprised and we can't work it out. This is completely contrary to the science it is completely contrary to public consultation," she said.

She leads an alliance of 25 environment groups called Save Our Marine Life who oppose the plans.

"We're very concerned that Australia's marine parks are proposed to have half of the sanctuary zone protection removed under these plans," Ms Grady said.

"That would be a precedent in Australia and a global precedent."

Federal National Parks director Sally Barnes said the latest plans protected biodiversity but also limited the impact on local industries.

The whales in Geographe Bay are a major drawcard for tourists. ( ABC News: Louisa Rebgetz )

She said describing the plans as a "cut back" were false.

"There have been proposals for different configurations of zoning but there are not any zoning restrictions or regulations in place in most of the Commonwealth waters," Ms Barnes said.

"When we get them operational, we'll have one of the largest areas of protection in no-take zones in the world.

"The same number of conservation features are protected in green zones in the plans released today as those in 2012."

'No real protection' for Coral Sea reefs

The Coral Sea off Queensland, considered the jewel in the crown of the 2012 network, is a key sticking point, and is home to more than 40 reefs which are a haven for marine life.

Tuna caught in the Coral Sea off Queensland. ( ABC News: Mick Fanning )

Diving operator Craig Stephen said the Osprey, Holmes and Flinders reefs in the Coral Sea were crucial areas, particularly for sharks.

"None of these reefs have been offered any real protection," Mr Stephen said.

"There's [an] amount of protection at Osprey reef, which is an iconic reef, but the other reefs for the most part have been left exposed to extractive practices.

"There is no balance — the balance is in favour of extractive practices."

Fisherman Pavo Walker relies on fish caught in the Coral Sea to keep his business going. ( ABC News: Mick Fanning )

But not everyone is against the changes proposed in the draft plans and fisher Pavo Walker is among those who welcomes them.

He owns the largest wild-caught tuna fishing operation in Australia, based at Mooloolaba on Queensland's Sunshine Coast, and relies entirely on the Coral Sea to survive.

Mr Walker said the 2012 plans would cripple the industry.

"The 2012 … model would have seen a complete end to our fishery and our industry and we are talking about a world gold standard sustainable fishery that would have been closed for emotional reasons, not scientific," Mr Walker said.

Mr Walker uses a longline with thousands of baited hooks that are left at sea for several hours to catch large tuna and swordfish.

Pavo Walker's crew at Mooloolaba with fresh tuna caught in the Coral Sea. ( ABC News: Mick Fanning )

The bulk of the catch is exported to Japan and the United States.

"When you start putting boxes all around the ocean and our gear drifts into them it becomes unfishable," Mr Walker said.

He said Australia imports a large proportion of fish from overseas markets where there were not the same sustainability standards.

Ms Barnes said areas that needed protection would be protected.

"When these plans go into place we will have reduced commercial fishing in selected areas where we think the conservation values are so high that we need to protect them from any extraction and that's an area about the size of Victoria approximately," Ms Barnes said.

It will be Federal Environment Minister Josh Frydenberg who will have the final say before taking the plans to Federal Parliament, but getting it through the Senate may prove a challenge.

The draft management plans are open for consultation until September 20.