Prominent Aboriginal leader, Galarrwuy Yunupingu has said life was better for Aboriginal communities when they were run by missionaries, in the 1950s and 60s.

While Mr Yunupingu does not want the missions brought back, he called for the Federal Government's intervention taskforce to set up dormitories to ensure children were properly fed, clothed and educated, after reporting they are going hungry and at risk of sexual assault and drug and alcohol abuse.

"The missionary days were good," Mr Yunupingu said. "The missionaries looked after the kids much better than the Government does today."

The Northern Territory's deputy chief minister, Marion Scrymgour echoed Mr Yunupingu. "Love, they (missionaries) did provide a lot of love and attention to those children. Maybe that's what's missing in some of our communities."

CMS missionary Steve Etherington says there is agreement on this issue in remote communities he has visited in his 28 years in the Northern Territory. 

"Almost all of them have fond memories of the mission era," he says. "They would have the missionaries back tomorrow if they could," 

Mr Etherington says missionaries did not try to impose "white ways' on the communities, but provided infrastructure and discipline.

"They tried to run missions on the cultural framework that people had " they certainly didn't try to attack pagan beliefs when they tried to evangelise people."

Missionaries to indigenous communities today need to "be compassionate without doing things for them that they need to do for themselves," he explains.

Mr Etherington adds that missionaries today can be most effective by translating the Bible into indigenous languages and training church leaders.

"The sooner we train Aboriginal evangelists and ministers, the better," he says.