It has an acclaimed academy programme, supported by 25 businesses and organisations, with Massey University and the Hawke's Bay District Health Board top sponsors.
"I struggle with the logic of rewarding the school that is pursuing excellence by actually taking away financial support for us," Mr Shortcliffe said.
"We have increased our attendance rates from 84 per cent to 93 per cent, which is pretty hard to do when you have had such a massive roll increase. We have reduced our suspension and stand-down rates over the last five years."
The funding cut will be spread over two years and represents 12 per cent of the school's seven-figure operational funding.
Mr Shortcliffe, a 2012 National Excellence in Teaching Awards winner, said he hopes to improve current programmes but will recommend to the board of trustees that voluntary school fees remain at $55.
The Government's expectation the school community cover the funding drop was "not realistic when you cannot seek fees formally".
"We are now going to have to think extremely strategically about our partnerships and our sponsors and our pathway forward. I would prefer my pure focus was on student achievement and not have to be distracted with fiscal management."
It didn't sit well that the Prime Minister could commend the school's success "and our reward for doing well is less funding, because apparently the community can pay for it, and a reduced principal's income".
Tukituki MP Craig Foss who visited Hastings Intermediate in 2012 with Prime Minister John Key said decile funding was independent of salary and property finances. He was confident the school would continue its "fantastic" achievements.
"The key message is it is no reflection on the school or its performance ..."
Education Minister Hekia Parata said the decile funding system was well intentioned but complicated and "a blunt instrument".
"There are many factors that make a good school good and it's important to remember that decile funding only accounts for about 12 per cent of overall funding for schools," she said.
"Decile ranking shouldn't be used as a measure of school quality or school performance."
NZEI president Judith Nowotarski said the fact that National Standards results aligned almost perfectly with decile ratings showed socio-economic background the biggest factor in educational outcomes. A more "sophisticated and fine-grained approach" was needed linking funding to socio-economic status, she said.
Hastings District Councillor Henare O'Keefe, a regular visitor to the school, said success leading to a mixture of student backgrounds was to be commended, not penalised. "They bring the classes together seamlessly ..."
The president of the Hawke's Bay Primary Principals Association, Michael Bain, said whether the school's lower funding was fair was "a tough question".
"If you have more students from homes with a low income they are going to require more support," he said.
"I sit in a decile 10 school and we receive pretty minimal government support and funding, because our community is expected to raise the difference.
"Is it fair? I don't know, but equally what is the alternative to address the inequities in society?"