The UN has ruled against listing the Great Barrier Reef as “in danger”, congratulating Australia on its conservation plan but giving it five years to halt deterioration of the natural icon.

Unesco’s world heritage committee in Germany on Wednesday unanimously passed an earlier draft ruling that the reef’s status remain unchanged but that Australia must show significant progress in pushing its plan by the end of 2016.

The committee praised Australia’s efforts but said it was still concerned about the threat of climate change, industrial port development and water pollution to the reef.

The environmental groups Greenpeace and WWF, which won praise for bringing concerns about the reef to the fore, told the committee it needed to maintain its scrutiny, given Australia’s support for the coal industry and “troubling signs” in monitoring water quality.

The committee chairwoman, Maria Böhmer, said Australia had done “everything in its ability” to engage with the committee’s concerns and its financial commitments were “a decisive foundation for preserving and conserving this brilliant world heritage property”.

But Unesco’s decision was not “the end of the debate, it’s just the beginning of a new phase” as focus turned to Australia’s implementation, she said.

Böhmer said she was convinced Australia would do so with “the greatest intensity”.

Australia came under fire for its care of the reef – which has lost half of its coral cover in 30 years and was on track to further deteriorate – in a tense meeting in Qatar last year.

But it won praise on Wednesday even from vocal critics including Germany and Portugal, with the latter saying that “today happily the future of this outstanding property looks much more promising”.

Committee members broadly commended moves to limit new ports on the Queensland coastline, ban the dumping of dredging spoil in world heritage waters and cut pollution runoff by 80% within a decade.

However, Germany noted the impact of dumping spoil from maintenance dredging for existing ports in reef waters, while Finland spoke of concerns about increased shipping.

The Philippines said Australia needed to address “knowledge gaps” in monitoring a reef 1,400 miles (2,300km) long and extend its vigilance in protecting coral to “seagrass beds, mangroves, floodplains and saltmarshes”.

The committee also heard that legislation and a detailed investment strategy still needed to be put in place by the Australian and Queensland governments.

Australia’s environment minister, Greg Hunt, said the country had “clearly heard the concerns of the world heritage committee” and implemented all its recommendations.

“In fact, the committee’s and in particular Germany’s interest and advice on the reef, has allowed us to do in 18 months what might otherwise have taken a decade,” he said.

Hunt said combined government investment in reef management and research would exceed A$2bn (£1bn) in the next decade with another A$200m in water-quality improvement.

“Having said this, like every reef, there are real challenges such as climate change and water quality, and that is why the new 2050 reef plan is a game-changing 35-year blueprint to protect and build the resilience of the reef,” he said.

Queensland’s deputy premier, Jackie Trad, told the committee that total government investment in reef management in the last financial year alone was A$485m.

Queensland’s minister for the Great Barrier Reef, Steven Miles, told the Guardian from Bonn that Unesco regarded its work around the reef as a “success story” but would be looking to see signs of improvement in its health by 2020.

“Particularly with the effect of restricted dredging, we would love to be able to demonstrate progress by then but really it’s the five-year horizon that’s going to be the best indicator,” he said.

Miles said the “proliferation of port developments” on the Queensland coast “was really what triggered” Unesco’s scrutiny of the reef’s world heritage status.

“Sometimes it’s easy to forget how far we’ve come on that. If three or four years ago you’d have introduced a complete ban on capital dredging [creating new civil engineering, such as ports, by dredging] apart from import ports, you would have had a riot,” he said. “But to the credit of industry and stakeholders, we’ve introduced that with relatively little controversy.”

Jess Panegyres, political adviser to Greenpeace Australia Pacific, asked the committee to “keep watching Australia” as its plan would not save the reef from the impact of an expanding coal industry onshore.

WWF Australia’s chief executive, Dermot O’Gorman, said the committee had “stood up for the reef with a very strong decision that places Australia on probation for the next five years”.

“It is the right thing to do until the actual condition of the reef improves. Plans alone won’t save the reef. The real work starts now,” he said.