The Northern Territory government should be careful about criticism of the federal government's budget priorities considering they provide the Territory nearly all of its funding, Senator Malarndirri McCarthy has said.

In the wake of Tuesday's budget, the NT's Treasurer Bill Yan said the government's measures let Territorians down, pointing to Labor's three NT federal politicians: Senator McCarthy, Marion Scrymgour, and Luke Gosling.

He said the lack of any mention in the budget about the Darwin Port meant it was clear "Labor has cut adrift their Member for Solomon, Luke Gosling".

"It is clear that Marion Scrymgour and Malarndirri McCarthy are also invisible to those calling the shots in the federal Labor government," he added.

Mr Yan said the NT has been short-changed despite billions in promised funding, with only $200 million for highway upgrades announced.

"All the Federal Government could commit was a conditional $200 million for a road that leaves the Territory on the hook for the rest," he said.

"Despite the growing momentum in our economy, we were given no confidence on our major infrastructure projects such as the AROWS project, supporting infrastructure for the Beetaloo Basin, and the Middle Arm Precinct.

"Billions of dollars have been promised for other parts of regional Australia, yet all the Territory got was maintenance money."

Speaking on ABC Radio on Wednesday morning, Senator McCarthy said Mr Yan and the CLP should be "very careful in terms of the kind of criticism" they pointed at the federal government when it provided 88.3 per cent of the Territory government's funding.

Noting comments from Chief Minister Lia Finocchiaro, who said the budget measures were "band-aid" and "maintenance" money, Senator McCarthy said the CLP had only been in government six months and had "yet to provide their first budget".

"We do inject significant funding into the Northern Territory as a whole," she said.

Under Senator McCarthy's First Nations portfolio, the federal government continues to fund, with both the NT Government and Aboriginal Peak Organisations NT, the Northern Territory Remote Aboriginal Investment, valued at $842.6 million.

The government has previously said the funding provides support for the delivery of essential services, including policing, health, women's safety and education.

The NT has the largest percentage of First Nations people in the country, 76 per cent of whom live in regional and remote areas. $55 million over four years has been committed to renew lease arrangements with the Traditional Owners of the jointly managed Booderee, Kakadu, and Uluṟu-Kata Tjuṯa National Parks.

The budget also features funding for food shortages for remote communities - the majority of which are in the NT - as well as remote housing and boarding schools.

"We're rolling out $50 million in terms of food security across regional and remote areas of Australia, and a large number of that is in the Northern Territory," Senator McCarthy said.

There is also the rolling out of remote laundries at a cost of over $11 million, with the long-term goal of eliminating rheumatic heart disease [RHD] from Indigenous communities.

"Certainly, [I'm] pleased with rolling out of remote laundries. I'm very concerned about that impacts so many First Nations people," Senator McCarthy said.

"And we know that something as simple as having more laundries in our communities and accessible has assisted and will assist in reducing and bringing those numbers down."