The announcement comes as formal hearings of the royal commission into the juvenile justice system are set to continue on Tuesday.
"NAAJA is the largest legal provider in the Northern Territory and has a strong track record in providing culturally appropriate services," Mr Brandis said on Monday.
NAAJA will provide referrals to solicitors, community outreach services and help potential witnesses access financial assistance.
NAAJA is contracted by the Commonwealth Attorney General’s Department (AGD) to provide Criminal and Civil Law services to Aboriginal people and their families in the Top End of the Northern Territory.
Prime Minister Malcolm Turnbull announced the royal commission after shocking footage of boys being tear gassed at the Don Dale Youth Detention Centre was aired on national television.