Museums Aotearoa is calling on local and central government to recognise the national significance of museums or some may need to close their doors.
A new study commissioned by Museums Aotearoa has found some museums have an average operating deficit of almost $280,000.
It also found museums and galleries were responsible for caring for 45 million items with a total value of $3.6 billion.
The sector body said years of decreasing visitor donations, coupled with rising operational costs, was causing widespread financial strain.
Museums Aotearoa chief executive Adele Fitzpatrick told Morning Report the research proved the true value of museums and the wide impacts they have - not only for society but for New Zealand's economy.
Museums of all sizes were at risk of having to close - with some large ones unable to attract the funding for large exhibitions and low visitor numbers.
They also did not have the volunteer base like some smaller museums did, Fitzpatrick said.
Councils have long used visitor numbers to quantify the success and interest in museums - but Fitzpatrick said it was a poor way to measure value.
"What we are asking for is central government to recognise the significant value that it receives from the sector."
It was a "financial reality" that some museums may have to close their doors.
"Many of the museums that I speak to on a daily basis are pretty worried about what's coming up."