Greens senator for Queensland Larissa Waters told The Guardian that dumping sledge into world heritage waters "treats our reef like a rubbish tip".
“The last thing the reef needs is more sludge dumped on it, after being slammed by the floods recently,” she said.
The permit allows 756,553 cubic metres of maintenance dredge sludge to be disposed of in the marine park and a further 200,000 cubic metres for sediments deposited by extreme weather events.
The announcement comes just weeks after extensive flooding in north and central Queensland that has deposited large amounts of sediment on to the reef.
The flood runoff could also affect seagrass and marine animals such as turtles and dugongs, a Senate committee heard last week.
Acting chief executive officer of the GBRMPA Bruce Elliot said the influx of water into the reef could lead to freshwater bleaching events and impact seagrass.
But despite these concerns, in a statement released last week, the North Queensland Bulk Ports Corporation said its assessment reports found "the risks to sensitive marine environments as a result of the maintenance dredging were predominantly low."
"The permits allow for the long-term, sustainable management of maintenance dredging at the Port and will safeguard the efficient operations of one of Australia’s most critical trading ports."
The GBRMPA added that the project would be monitored after each campaign.
"Applications for maintenance dredging and disposal of maintenance dredge material within the Great Barrier Reef Marine Park undergo extensive assessment looking at the social, economic, environmental and heritage impacts," a spokesperson for the GBRMPA said in a statement.
"The applicant’s peer-reviewed sediment assessment investigated whether maintenance dredging could be avoided, reduced or beneficially reused. Due to the nature of the material, it found there to be limited beneficial reuse options."
Maintenance dredging refers to relocating sediment that naturally accumulates in shipping channels, to ensure vessels can access ports and marinas.
In 2015, the federal government banned the disposal of dredging sludge near the reef, but this only applied to capital dredging which involves excavating previously undisturbed areas of seabed.