The report, published in The Australian newspaper on Saturday, said Aboriginal boys are 10 times more likely to be raped than the national average.
The Australian Medical Association's Territory branch has called for the army to be sent to Wadeye, one of the largest indigenous communities, where it is believed all 1,300 children are at risk of because of gang violence.
But the Wadeye community council said bringing in the army will not fix problems that have been brought about by chronic discrimination, substance abuse and poverty.
"That is rather ludicrous to suggest a peace-keeping role, that's sort of drawing a bit of a long bow," said Dale Seaniger from Wadeye's Thamarrurr Council, speaking to ABC radio.
However he said the community would welcome troops to help implement other initiatives, particularly infrastructure such as roads, housing and maintenance.
Wadeye has no high school and homes are drastically overcrowded, he said.
The NT government said the AMA's concerns will be thoroughly investigated, but dismissed the army idea.
The Federal Minister for Indigenous Affairs Mal Brough earlier this week called for an urgent summit to address violence and abuse in Australia's indigenous communities.
Mr Brough wants communities, state and territory leaders to attend such a meeting, after reports of sexual abuse and drug use within aboriginal groups.
But the Northern Territory's Chief Minister Clare Martin said she would boycott any summit.
However Mr Brough said it would be the only viable solution.
"Let's not pretend for a moment that this is not a disaster. What I would say to Clare Martin is admit what we have here, lift the scab of it and deal with the fundamental issue," he said.
The call for action come after the Crown Prosecutor for Central Australia revealed a number of cases of sexual abuse and drug use in the remote Aboriginal communities earlier this week.
Saturday's report was the culmination of an 18-month study by the Queensland University of Technology, in which 301indigenous men in the Northern Territory and Queensland were interviewed.
It found that one in 10 had been raped before the age of 16 -- 10 times the rate in the rest of Australia.
Researchers said that the abuse had largely remained a secret because victims were too ashamed or scared to seek help.
"It becomes a mirrored thing: if you abuse people and get away it, then you continue with it and then others learn from you," head researcher Mick Adams told the paper.