As part of the Environmental Protection Act, passed overnight, courts will be asked to consider the significance of the Great Barrier Reef to the nation when considering what penalty to hand down to those found to have wilfully harmed it.

It essentially identifies harm to the reef to be an aggravating factor to be considered by the courts in sentencing.

Maximum penalties for individuals have increased from $470,000 to $700,000, while corporations will face fines of more than $3.5 million, from $2.3 million.

Jail terms have also increased from two to five years.

"For the first time in Queensland legislation the Great Barrier Reef World Heritage Area is recognised as being special and as such the court needs to take that into consideration when looking at the charge and the penalty," Environment Minister Andrew Powell said.

"What it targets is particularly industrial activities along the coast that could have an impact on the World Heritage Area and that's the simplest way to put it. There has to be a wilful attempt to harm the environment.

"It steps up the possible penalty for an individual or company. If someone does something that harms the world heritage are, that is taken significantly."

But the Opposition said the change does nothing to protect the reef.

"The amendments moved at the last minute by Minister Powell do nothing to address the significant threats faced by the Great Barrier Reef and represent more spin by the Newman Government," Jackie Trad said.

"Over the past two years, the Newman Government has wound back important environmental protection laws put in place to reduce sediment run-off, protect the Reef coastline and amended the Abbot Point expansion plan so that all dredge material would be dumped at sea.

"The Environment Minister and the Newman Government have had many opportunities to reverse their environmentally damaging decisions, including today but, instead introduce ineffective laws to give the impression that they care about the Reef."

Mr Powell said the government had gone over and above international expectations to protect the reef.

"It's part of our ongoing commitment to ensure the Great Barrier Reef is the wonderful natural icon that it is not only to Queensland and Australia but to the world," he said.