But Ms Main said she was sure online voting would be an option in the 2019 local body elections.
It was estimated the trial would have cost the district council an extra $75,000, but the trial wasn't supported by either the Whanganui District Health Board or Horizons Regional Council. The council's electoral officer manages the vote collection for both those authorities.
Ms Upston said timing restrictions meant preparations for the trial had not met legislative requirements and Government "cannot guarantee public confidence in the election results".
She said security testing was planned but had not yet taken place, and without seeing the results of testing Government could not be confident the systems were secure enough.
The other councils interested in trialling online voting included Selwyn, Wellington, Porirua, Masterton, Rotorua, Matamata-Piako and Palmerston North.
Ms Upston said the Government was open to looking at online voting in the future.