Belfast Coastal Reserve is a 20-kilometre stretch of coastline between Warrnambool and Port Fairy and is, according to Parks Victoria, "known for its wild and unspoilt nature".

It is an important breeding habitat for the hooded plover, which nests on the beaches, and is considered a resident bird of the reserve. It is also among the top 20 priority birds in the federal government's threatened species strategy.

The reserve is also rich in cultural heritage, including coastal middens and stone artefacts which are evidence of tens of thousands of years of occupation by Eastern Maar people.

It was used for decades by local horse trainers, an activity which opponents say threatened the hooded plover as well as cultural sites.

The long-running tussle over beach use between horse trainers, birdwatchers, surfers, Indigenous people, fishers and recreational users appeared to have been settled in July when the government finalised its Belfast Coastal Reserve Management Plan.

Under the plan, year-round commercial horse training was allowed at Levy’s Point. Up to 120 horses a day would be allowed to train on the beach with an additional 40 horses a day permitted to access nearby Hoon Hill via Levy's.

The plan also created conservation zones where horses were banned.

But that outcome was turned on its head in October when the Warrnambool City Council revealed it had received legal advice that horse training on Levy's Point was prohibited under planning laws, just days after councillors voted 4-3 in favour of allowing the activity.

The beach was already slated as Public Conservation and Resource Zone and the local council – which manages the land around Levy's – said that existing zoning prohibited animal training.

This prompted the minister's intervention in December. On December 16, Mr Wynne wrote to councillors, advising them he was going to use ministerial power to amend the Warrnambool Planning Scheme to remove the prohibition. Five days later, the council held a meeting to back his plan.

That site-specific planning control came into effect this week, and denies community members their normal rights of objection or appeal.

Brad Jessup, a University of Melbourne expert in planning and environmental law, said the minister's decision to exercise his power to "convert a particular prohibited use into a permitted one" was "unusual" and had not followed a "robust or rigorous [process] at all".

He said site-specific planning controls were more often used for special projects in the public interest, such the Commonwealth Games Athletes Village.

"The worrying part of this tale is that the community goodwill in taking part in the management plan process has been one of the reasons for them losing their powerful rights under planning law," Mr Jessup said.

"That is a terrible outcome for our democracy.

"It is why I too often counsel communities to be cautious in taking part in forums or to participate in non-legal processes. The story in the past has been that these processes are set up to appease, then to disempower communities."

Belfast Coastal Reserve Action Group's Bill Yates, who took part in the consultation advocating for a ban on horses, said he felt as if the intervention "shifted the goal posts" and "was dropped on the community five minutes to midnight, just before everyone went on holidays".

"It sets a pretty terrible precedent. There are a lot coastal areas zoned exactly the same way. If it can be done here, it can be done anywhere," he said.

But Warrnambool Racing Club chief Peter Downs said the intervention was simply rectifying "an anomaly in the planning scheme which was missed in the process".

He said the state government had done a good job in committing to a lengthy consultation, and had considered all users and concerns, including environmental ones.

Mr Downs said he hoped to have horses back onto the beach as soon as practical.

"It will be a very big positive for the local industry and, most importantly, give a bit of surety around a matter that has had a lot of insecurities," he said.

A Victorian government spokesperson said Mr Wynne was on leave, and did not answer questions.

"We’ve been working hard to make sure we get the balance right between the environment, indigenous heritage, training and the need to protect the significant benefits that the racing industry brings to the south-west," the spokesperson said.

"More than 800 people have participated in community consultation and we’ve taken advice from the council who have endorsed amending the local planning scheme to enable horse training on Levy’s beach."