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Alliance representatives met Rural Communities Minister Damien O'Connor yesterday, making their case for $600,000 for the organisation, which manages a range of rural health projects.
However the bid, equivalent to $1 for each person living in rural New Zealand, was not accepted.
"We are bitterly disappointed," alliance chairman Martin London said.
"We thought our cause was robust ... but unfortunately they haven't come up with any straight funding, which leaves us in a hugely difficult situation."
Last week the alliance ran out of money and suspended all work other than existing, funded contracts.
"It has now become somewhat urgent because we haven't got enough to come and go on any more," Dr London said.
"We got a fairly clear message that there's not a cheque book and there's not money coming, but at the same time they were keen for our existence to continue."
The alliance board has previously resolved to wind down if it did not receive government funding - as the world's other two rural health networks, in Australia and the United States, do.
"In Australia the funding actually came first, stating get yourself organised because we want a straight conduit to the rural community," Dr London said.
"That's not how it happened in New Zealand, and up till now we have had to rely on subscriptions, organisations and contract work, which doesn't pay for infrastructure."
The alliance is a registered charity, and its initial set up and running expenses were funded by membership fees and sponsorships.