A Larrakia elder says the proposed Charles Darwin University city campus will be "cursed" after university contractors removed a remaining historic milkwood tree in the early hours of Sunday morning.

Key points: On Saturday morning after the first milkwood tree was removed, a small protest assembled at the site

On Saturday morning after the first milkwood tree was removed, a small protest assembled at the site At that time, NT Police stood down workers to seek clarification over the remaining tree's heritage status

At that time, NT Police stood down workers to seek clarification over the remaining tree's heritage status A Charles Darwin University statement described the move to remove the trees as a "unanimous" decision from CDU, the City of Darwin and the NT Government

The 100-year-old milkwood removed on Sunday had survived multiple cyclones including Cyclone Tracy, but it was the proposal for a $250 million university campus in the Darwin CBD — the crown jewel of the Darwin City Deal — that it wouldn't survive.

Larrakia man Eric Fejo was responsible for nominating four city milkwood trees for heritage protection, including the two trees that were cut down over the weekend.

He said he wasn't contacted by CDU, the City of Darwin or the NT Government to be told that two of the trees he'd nominated for special protection would be removed and said he was "gutted".

"My belief is that these trees have got spirit in them, and this spirit's been cut down, and so this spirit is going to be unrested," Mr Fejo said.

"So this place as far as I'm concerned is cursed and they're going to build a place for educational purpose and it's cursed."

After a protest prevented its removal yesterday, a historic milkwood tree in the Darwin city centre has been cut down in the early hours of this morning. ( ABC News: Kate Ashton )

'They don't understand what they've done'

Mr Fejo said the milkwood trees were special to him and his family, which is why he had nominated them for heritage status back in September.

"This place is very special because my father was born just over there," he said.

"This is on top of frog hollow and people used to sit down up here, under these trees, these ancient trees, they're ancient.

"I just hope these people sleep good at night you know.

"This is generational — they don't understand what they've done."

He said he was encouraged by the support he had seen of the trees from other Darwin residents including the non-Indigenous community, and outrage on social media.

After a protest prevented its removal yesterday, a historic milkwood tree in the Darwin city centre has been cut down in the early hours of this morning. ( ABC News: Kate Ashton )

"There are people that do care, I'm looking at them now, and I'm really glad," Mr Fejo said.

"They might not believe in some of the stuff we believe in, but that's fine," he said.

Confusion over heritage status

On Wednesday CDU, the NT Government and the City of Darwin welcomed a conditional $150 million loan from the Northern Australia Infrastructure Facility which would help fund the new campus.

It was this funding which CDU said enabled them to begin preliminary works, such as tree removal this weekend.

Independent MP Gerry Wood led a small protest against the tree's removal on Saturday. ( AAP )

On Saturday morning after the first milkwood tree was removed, a small protest assembled at the site, led by independent MLA Gerry Wood, which prevented CDU contractors from removing the second milkwood tree.

At that time, NT Police stood down workers to seek clarification over the remaining tree's heritage status, leaving some with the impression that the tree would have a chance to go through the formal heritage assessment process before being removed.

It's a process that can take months, but that could have seen the trees granted provisional protection at the Heritage Council's next meeting in March — if they deemed the trees were significant.

The NT Heritage Branch confirmed the four milkwood trees had been accepted for heritage nomination on December 6, but that this stage didn't afford them any legal protection.

A Charles Darwin University statement described the move to remove the trees as a "unanimous" decision from CDU, the City of Darwin and the NT Government "following consultation with Larrakia Nation".

It said the site wouldn't be suitable for the campus unless the two milkwood trees were removed.

After a protest prevented its removal yesterday, a historic milkwood tree in the Darwin city centre has been cut down in the early hours of this morning. ( ABC News: Kate Ashton )

A statement from NT police confirmed "the removal of the trees was lawful".

Memories of Hotel Darwin

MLA Gerry Wood returned to the site this morning, to see that the tree he had protested for yesterday had been cut down before any supporters could arrive to save it.

He said the idea that this was done early on a Sunday morning is sure to make residents furious, and invoke painful memories of the surprise demolition of the Hotel Darwin.

"It's just an act of bastardry, the people who live in this city, have been left out of this whole consultation process," he said.

"Whether it's the university, the council, the NT Government or what, they've made some decisions about this piece of land, and they've not included the people who lived here."