The NT's decision came after the Federal Government's Pharmaceutical Benefits Advisory Committee (PBAC) concluded that it would not be cost-effective to provide the rotavirus vaccine to all Australian babies.
Babies born in the NT after August 1 will now be routinely offered an oral vaccine against rotavirus - the leading cause of diarrhoea-related illness and death among children and infants internationally.
"This is great news and the AMA congratulates the NT Government for taking this important action," Dr Haikerwal said.
"Hopefully the NT Government's smart move will provide the impetus for other States and Territories, but preferably the Federal Government, to fund rotavirus vaccinations for babies.
"If they can't fund the vaccine for all babies, they should at least provide it for those most at risk, such as babies in tropical and semi-tropical areas, and babies of Aboriginal and Torres Strait Islander descent."
A recent AMA Executive Council resolution urges the Federal Government to fund the rotavirus vaccine as a matter of urgency for all Indigenous children.
"Although the PBAC has decided it would not be cost-effective to give the vaccine to all Australian children, there are vulnerable groups for whom it would not be a huge strain for governments to provide immunisation," Dr Haikerwal said.
"It would be tragic if Indigenous babies living in the north of South Australia miss out on vaccinations while those living just across the border in the NT are immunised, when they all face the same risk of contracting the disease."