"Due to timing restrictions, preparations for the proposed trial have not yet met the legislative requirements and cannot guarantee public confidence in the election results.
"Security testing has been planned but has not yet occurred. Without seeing the results of testing we cannot be confident the systems are secure enough, and the trial could not be authorised."
Ms Upston said online voting could be trialled at future elections and the Government was open to looking at proposals for future trials.
Rotorua mayor Steve Chadwick said it was a missed opportunity.
"For us it was an opportunity to engage with different parts of the community and we saw online voting as something that would appeal to them. We believe it would have made it easier for people to vote using technology they are comfortable with using."
Mrs Chadwick said the council understood systems needed to be secure and reliable and it had invested more than $25,000, plus a further $6000 in staff costs, to comply with Department of Internal Affairs guidelines.
"Our work, as requested, was on assuring government officials around the perceived security risks and we were able to do that," she said.
Rotorua District Residents and Ratepayers group mayoral candidate Dr Reynold Macpherson, who had made submissions to the government against the trial, said he was pleased with the decision but unhappy the council had wasted ratepayer money before the decision was announced.
"Our action research team led by Paddi Hodgkiss campaigned against online voting on the grounds cited by the Minister. But we now hear that the council went ahead and spent $31,000 preparing for the trial.
"They refused to accept international research showing that online voting makes very little difference to voting patterns. The council should apologise to ratepayers for its grand-standing and extravagance," he said.
The council's youth portfolio leader, councillor Tania Tapsell, said it was a big disappointment.
"If we can safely do our banking online I don't see an issue with online voting. The feedback from our community, especially our youth, was that they were all for it. With a poor voter turnout we wanted to get those numbers up," she said.
The other councils involved were Selwyn, Wellington, Porirua, Masterton, Matamata-Piako, Palmerston North and Whanganui.