A Darwin pool will still be extended, but much more important uses for Commonwealth National Stronger Regions Funding are in doubt.

The Roper Gulf Regional Council was not awarded a recent round of the $212 million federal funding scheme, throwing the future of proposed regional transport hubs in the NT communities of Ngukurr, Numbulwar, and Borroloola into darkness.

The proposed transport hubs are a major project in the Northern Territory, and one that locals say deserve a share of the grants.

Roper Gulf Mayor Tony Jack says $1 million in co-funding had been secured from the Northern Territory Government, but is now on hold.

Meanwhile, the $4.48 million grant to extend a Darwin swimming pool by 50 centimetres will continue.

The pool funding is the Territory’s only successful project to get a share of the $212 million funding scheme.

Mr Jack said pool upgrades are fine, but the Commonwealth Government has “lost focus on where regional and remote Australia really is”.

“[The Department of Infrastructure and Regional Development] see Darwin as regional, we don't see Darwin as regional,” he told the ABC.

“So [we're asking] what that makes us then, out here in the bush, do we exist?

“For one [grant approval] in the Northern Territory it's a big disappointment for us over all, I'm talking for all councils.

“At least some of us should have got something out of it.”

Mr Jack said he had not been told why the council's grant was rejected.

“It was a big disappointment in the end, really frustrating,” he said.

“We put up this big, you beaut proposal, trying to get everything right and to get nowhere with our submission, it doesn't sit right with us.

“I wonder where the fairness is with regional communities.”

The Department of Infrastructure and Regional Development responded to inquires on the matter in a fairly generic statement.

“The Fund is highly competitive, as evidenced by the 405 applications received for Round One which sought funding of more than $1.2 billion,” the statement said.

“In the end 51 projects were chosen under Round One, sharing in more than $212 million in funding.

“The programme is directed to disadvantaged areas, and submissions are assessed on a merit-based system.

“Round Two of the National Stronger Regions Fund is now open.”