The criticism came as federal Health Minister Mark Butler admitted "something has gone wrong" to allow such an outbreak when most developed countries had relegated the disease to the "dustbin of history".
More than 230 diphtheria cases have been recorded across Australia in mostly Indigenous communities in the year to date - about 30 times the usual yearly average.
About 60 per cent of cases of the potentially deadly disease have been in the Northern Territory, with more infections in Western Australia, South Australia and Queensland.
The outbreak has triggered a $7.2 million federal cash injection to help control the spread as authorities stressed the importance of getting vaccinated.
The National Aboriginal Community Controlled Health Organisation, representing 148 Aboriginal community health services, said the government response initially took too long.
The organisation's chief executive Dawn Casey said the group began lobbying government to take action in early April.
"We were really concerned about how fast it was spreading," she told the ABC on Friday.
The government had finally responded in a comprehensive way but it took them weeks to do so, she said.
"They just do need to, in future, respond much more quickly than they have."Mr Butler said the causes of the outbreak would be examined in due course but the focus now was on containing the disease by getting needles into arms.
"Obviously something has gone wrong to have a disease that most developed countries have assigned to the dustbin of history," he told ABC Radio National.
The funding package covers a surge in medical staff to affected regions and the free provision of vaccines and antibiotic treatments after the outbreak highlighted a shortfall in health workers in remote communities.
Mr Butler said he suspected staff shortages, vaccine hesitancy and overcrowding in remote communities may all have contributed to the outbreak but it was too early to reach conclusions.
"Some of the social determinants, they are largely centred on remote and very remote communities where there are issues of overcrowding and sanitation."
Vaccination rates for First Nations children were higher than for the general population and a large number of diphtheria cases were of adults who hadn't received booster shots.
NT Health is waiting on autopsy results for a suspected diphtheria-related death in the territory.
Health Minister Steve Edgington and his department have been accused of being missing in action in responding to the outbreak.
But he rejected the criticism on Friday, telling reporters there had been press conferences, the chief health officer had communicated regularly with the media and a range of material had been circulated.
Indigenous Australians Minister Malarndirri McCarthy told reporters in Sydney she had her diphtheria booster shot on Friday, making the point that adults had to make sure they were up to date on their jabs.
"I just urge Australians everywhere, please get vaccinated."
Diphtheria often begins like a bad cold but can quickly turn deadly.
The bacteria produce toxins that can form a thick grey layer in the throat, block the airway and cause suffocation.
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