One person from Perth voted for the Shag more than 300 times overnight, catching the attention of competition organisers.
The online voting system only allows one vote per email address for New Zealand's birdlife.
Bird of the Year spokesperson Laura Keown said the illegal votes have been wiped.
"We often have some small voting scandals but we're always on top of them.
"I think it's great that people are excited about getting exposure for their favourite native birds because there's a biodiversity crisis in New Zealand," Ms Keown said.
Last year the White Faced Heron found itself on the receiving end of a similar voting scandal which was quickly rectified by the organisers.
The Kea was eventually crowned New Zealand's Bird of the Year for 2017.
In 2015 two 15-year-old girls created a number of fake emails and flooded the competition's voting system with fraudulent votes for the Kōkako.
As it stands, the Kererū is in the lead with more than 3300 votes with the Kākāpō a thousand votes behind in second.
Voting closes next Sunday with the winner announced on Morning Report the following Monday.
