Environmentalists and some scientists say dredge spoil will harm the Great Barrier Reef.
A former senior director with the Great Barrier Reef Marine Park Authority has spoken out against the department's decision to allow dredge spoil to be dumped in the marine park off Abbot Point.
Earlier this year the authority issued a permit for North Queensland Bulk Ports to dump three million cubic metres of dredged seabed offshore as part of a project to turn Abbot Point into one of the world's biggest coal ports.
The decision followed Federal Environment Minister Greg Hunt's approval of the expansion.
Environmentalists and some scientists say the dredge spoil will harm the reef, while the federal government says developers must adhere to strict environmental conditions.
Jon Day, a former GBRMPA senior director, opposes the decision and the way it was made.
"I believe there were alternatives that weren't properly considered when that decision was made," he told ABC's Four Corners which aired on Monday night.
"If we did a proper evaluation of all the alternatives, that decision would not have been made."
Mr Day, spent two decades with the authority before resigning this year, said the spoil shouldn't be dumped within the marine park.
"Our own legislative mandate says 'the long-term protection and conservation of the values', and we're not doing that," he said.
Mr Hunt said his advice was that disposing the spoil was safe.
"I did a very careful and deep review and what was clear is that we could tighten and strengthen the conditions," he told the ABC.
GBRMPA chairman Russell Reichelt said he doesn't believe the project will harm the reef.
"The risks around Abbot are low and approvals were given on that basis that they are manageable," he said.
Internal emails obtained under Freedom of Information reportedly show that up until January this year GBRMPA experts were against the proposal.
Mr Reichelt told the ABC he had encouraged staff to air their views.
"The project changed considerably over the life to something that at the end a decision was made taking all of that into account that that disposal could occur safely," he said.
In June next year the World Heritage Committee will decide if the reef should go on its "in danger" list.