The maps, obtained by ABCRural, draw up a large network of proposed marine parks right around Australia, particularly off the coast of Queensland and north and south Western Australia.
But the Resources Minister Martin Ferguson has been approving new mineral exploration licences near some of these areas, reports ABC Rural.
Chris Smyth, from the Australian Conservation Foundation, says he's hoping the ministers are working together.
"In terms of Minister Ferguson's process, yes, we've been very concerned that he's been rolling out areas to give access to the oil and gas industry, while Tony Burke's marine planning process has been going on, and we've certainly made that clear to the government," he said.
"But it would seem as though both ministers are working together in some ways to ensure that we can get some increased protection."
Neither minister was available for comment.
The Queensland Seafood Industry Association says it's concerned that such large areas of the Coral Sea off the coast of Queensland could be locked up.
Spokesman Geoff Tilton says tuna fisherman will be hit hardest, and prawn trawlers will also be affected.
Questions Raised Over Proposed Marine Parks
AUSTRALIA - A map of proposed new marine parks has some questioning whether the federal environment and resources ministers see eye to eye.
by Lucy Towers