Ship accidents on reef will happen: Joyce

Barnaby Joyce has rejected calls for new restrictions on cargo ships coming through the Great Barrier Reef, saying it would ruin the economy and ignores the fact accidents happen.

Federal Environment Minister Josh Frydenberg announced on Monday the government had reached a $39.3 million out of court settlement from the operators of the Shen Neng 1, which ran aground 100km east of Rockhampton at Douglas Shoal in 2010.

The money will be used to remove polluted rubble in a clean-up operation expected to begin next year.

The government had been seeking at least $120 million from Shenzhen Energy Transport Co Ltd.

Greenpeace Australia says it shows "coal and the reef don't mix" and the government must do more to protect the area.

The acting prime minister said it was important the remediation work began quickly, but he did not believe new checks were needed.

"The thing I wouldn't want to do is start coming up with new reasons for not having ships come into Gladstone or Townsville or Mackay, because ... I want there to be a vibrant economy," he told reporters in Townsville on Tuesday.

"There will be further accidents in the future, there's no doubt about that - but that's life.

"If you have ships at sea you're going to have them run into things and sink from time to time."