Approval was granted prior to the plant being recognised as endangered so the approval stands.

Planning approval was granted in March 2014, subject to a search for endangered species. Species of hibbertia, or guinea flower, had been found in a Holsworthy military area survey as far back as November 1999 but not identified as the extinct variety.

Stage 1 of the Intermodal was approved on Monday, December 12 and announced the following Wednesday.

Two days later, on the Friday, the hibbertia species was provisionally listed as the critically-endangered fumana – four days too late to stall the approval process.

The federal Environment department said in a statement that "new species listings do not affect pre-existing approvals”.

Greg Hunt, the former federal environment minister, gave planning approval to the SIMTA Moorebank Intermodal terminal in March 2014 but imposed conditions on the rail-freight plan, including a "targeted search" for an endangered species of hibbertia flowering plants.

The search instead found 370 individuals of the hibbertia fumana species on the seven-hectare site, formerly owned by the military and largely untouched.

The plant was thought to be extinct and last documented in 1823. It was only named in 2012 as a separate species from pressed specimens held in overseas vaults.

"Finding a species thought to be extinct is not something many scientists get to do in a lifetime so this is an exciting discovery for everyone involved," said Jane Rodd, a senior ecologist with Arcadis, the consultancy hired to do the search.

Why is this plant important?

One of the insiders interviewed for this story, who asked not to be named, said: “It’s unique, it has a value and a right to exist. It’s remarkable to go out in Western Sydney and see a plant that may not exist anywhere else on earth.

“The flower is about the size of a 50c piece. The function of this plant is mostly unknown, but insects, including bees, rely on it. A traditional bee can’t pollinate this one.”

But rather than trumpet the rediscovery, claims from within the Office of Environment & Heritage have arisen that staff were told to keep the finding a secret until the Intermodal won approval – which it did from the Planning Assessment Commission on December 12 last year.

Mark Speakman, the environment minister until the appointment of Gladys Berejiklian as the new premier, said he was unaware of the flower's status.

"Neither I nor my office gave, or was aware of any, direction about dealing with any discovery of hibbertia fumana at the Moorebank site," he said.

An Environment spokesman said it was not his department's role to inform the planning commission of the fumana rediscovery.

Despite the federal demand for a study, the planning commission’s report made no mention of hibbertia.

The plant was granted a "critically endangered" emergency listing by the NSW Scientific Committee four days after the planning commission ruling. 

"This area of bushland where the plants have been found is proposed to be set aside as a biobanking site as part of the adjacent development," the Environment spokesman said.

"The species has only been found on the proposed biobanking site and not in the development footprint," he said, adding the government was working with the alliance behind SIMTA and the Commonwealth "to ensure the security of the plants".

On behalf of the Intermodal, a SIMTA spokesman dismissed a claim the proposed development would run through some of the hibbertia plants. He released this chart showing the plants falling within a proposed conservation area:

“The simple fact is not one of the 370 hibbertia fumana plants our ecologists discovered is on land to be developed,” he said. “The entire population is on adjacent bushland already set aside for conservation.

“There is no threat to this rare herb on our site. Its protection and ongoing management are guaranteed under plans being developed with state and federal environment agencies.

“Thanks to flora surveys done as part of the Moorebank development, a plant last seen in the 1820s is back from presumed extinction and its future protected. We think that is a very good thing and are pleased to have played a part.”

Wayne Olling, secretary of the Cumberland Conservation Network, said the government should let outside groups such as his own examine whether the plants would indeed be secure.

"Here's an opportunity to save a species that we thought was lost and now found," he said. "The NSW government should have informed the PAC that there was a significant finding. Given all the concealment that's taken place so far we have no confidence in what they say.”

Labor, the Greens and the NSW Nature Conservation Council said the project needed to be reviewed after the finding of the rare plant.

"Any attempt to withhold information during the planning process is a very serious matter," said Penny Sharpe, Labor's environment spokeswoman, adding Minister Speakman "must  publicly guarantee that there has not been any interference in the planning process either directed by his office or his department".

Mehreen Faruqi, the Greens environment spokeswoman, said there was "something very dodgy" about this whole thing. "We need to know who knew what and when as well as how the project was approved just a few days before this critically endangered species was listed," Ms Faruqi said. 

"The environment minister needs to press pause and understand that this species occurs only on this site and if it is bulldozed then it is likely gone from this earth forever."

Kate Smolski, chief executive of the conservation council, said it was unacceptable that the federal government approved projects before the full environmental impacts were known and a stop-work should now be imposed on the project.

The process also revealed "systemic failures" on the part of the NSW planning system, she said.

"The government should also explain why it took until mid-December to list the species as critically endangered when it was rediscovered on the site more than a month earlier," Ms Smolski said.

"It is hard to avoid the conclusion the NSW government delayed listing the species to ensure the project went ahead as scheduled."

Local Greens spokeswoman Signe Westerberg said: “What right has the government got in delaying any findings? We need the best outcome for the whole community – for humans, for fauna and for flora!

“I’m pretty disgusted. When a company pays for its own investigation how can that be independent? And the biobank is a bit of a furphy. How can it be a biobank if it has a railway line through it?”

Fairfax Media sought comment from Josh Frydenberg, Mr Hunt's successor in Canberra.

The federal Environment department, though, echoed comments of its state counterparts, saying that no fumana plants were within the development site.

An offset site is being prepared so that the fumana "are not impacted by the project and will be protected in perpetuity", the department said in a statement.

Since the plant was not listed – as it was thought to be extinct – its discovery "will not trigger any review of the project's approval", the government said, and "new species listings do not affect pre-existing approvals”.