More than 250,000 crown-of-thorns starfish have been removed from the Great Barrier Reef off Queensland in the past two years, Federal Environment Minister Greg Hunt says.

The pest is considered to be one of the biggest threats to the reef and has traditionally been hard to destroy.

In recent decades, the crown-of-thorns starfish has been responsible for 42 per cent of coral loss on the Great Barrier Reef.

Researchers are now using a single injection that causes the starfish to break up between 24 to 48 hours, replacing the previous method requiring up to 20 injections.

The single injection method is harmless to other marine plants and animals.

Mr Hunt says the method has lead to a four-fold increase in the eradication rate.

"We have provided $1 million now - we have $2 million in the budget going forward and we believe that this is likely to be an ongoing program," he said.

"It's necessary for the reef and it's the single best hope we've had in dealing with the crown-of-thorns since people have been working in this space."

Mr Hunt says the new method has made a big difference.

"This is a nasty critter - it does damage to the reef, it does damage to aquatic life," he said.

"We can make a difference - we have saved literally billions of eggs from being released onto the reef."

Crown-of-thorns cull part of long-term reef plan

The Government's crown-of-thorns eradication plan is a key element of its Reef 2050 Plan.

Divers from the Association of Marine Park Tourism Operators can cull over 1,000 crown-of-thorns starfish on a 40-minute dive.

Project manager Steve Moon says this includes 27,000 in just eight days at Arlington reef and 9,000 at Batt reef, as well as 14,000 at Spitfire reef near Cooktown, north of Cairns.

"What we have noticed is a significant increase in coral cover, which is absolutely spectacular," he said.

Mr Hunt says the method has lead to a four-fold increase in the eradication rate. ( ABC News: Kirsty Nancarrow )

"That was the aim of the whole program - to try and give the coral a chance to grow and we've seen that, despite some of the extreme weather events that we've had."

Other measures under the Government's Reef 2050 Plan will see improvements to the quality of water entering the reef, which will limit the ability of larval-stage starfish to thrive on water-borne algae that results from nutrient-rich waters.

The Government has also funded a second control vessel, Venus 2, as part of the program.

But Mr Moon says more resources may be needed.

"I don’t think we’ve seen the peak of this current outbreak yet," he said.

"I think we’re going to be looking further down the track somewhere around this time next year, given that we’ve already had a spawning season in recent months.

"What we’re going to see - is two boats going to be enough? Possibly, but probably not."

Jairo Rivera from James Cook University helped to develop the single injection and says it is working with scientists from the Sunshine Coast University on a contraceptive to further control the spread of crown-of-thorns starfish.

"We found a protein on the surface of the sperm and that can be [bound] to a molecule that turns the eggs sterile," he said.

"If we can do that, that will be awesome because one single starfish can produce up to 60 million eggs per year."

Mr Rivera says the new method could be ready to trial in two years but $300,000 is needed to support the research.