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The Southern District Health Board area had 47% coverage of this group as of July 3, compared with 60% for the non-Maori and non-Pacific population in the same age category.
In a letter to the board, director-general of health Ashley Bloomfield said the disparity was concerning.
"It is vitally important that we protect our vulnerable kaumatua [elderly]," Dr Bloomfield said.
Southern DHB chief Maori strategy and improvement officer Gilbert Taurua said the board was committed to improving immunisation rates for all age groups.
"During the last few months, Covid-19 has impacted on the timely planning and delivery of health services and magnified the larger pandemic of social inequities in health," he said.
Much of the immunisation work is carried out by primary health organisation WellSouth.
"While there are questions around the accuracy of the data capture, we acknowledge Dr Bloomfield’s concerns and are working together with WellSouth to improve our performance with pop-up marae clinics and other targeted initiatives," he said.