The NFU pulled the poll, which asked 'should the Agriculture and Horticultural Development Board (Levy Board UK) back the Red Tractor?', after it received more than 1,000 votes, with more than 75% saying no.
However, the organisation said around 600 of those no votes had come from a single computer server, belonging to the MLC, in batches of up to 30 at a time.
NFU spokesman Anthony Gibson said at the time: "We noticed shortly after it was put on the website that it was getting vastly more visits than most other polls we've put up.
"It was being sabotaged, so we decided to pull it and I have to say its rather sad that what was a genuine and honest attempt to take the temperature of opinion amongst farmers was subverted in the way this was."
However, the MLC has denied any conspiracy, stating the most likely cause was a computer glitch.
A spokesman said: "The NFU has raised with us the issue of block votes coming from the MLC/EBLEX computer server.
"The IT experts in MLC and NFU are currently undertaking a forensic examination of the computer systems to establish whether it was an IT glitch racking up multiple votes when single votes were cast, or if there was something more malicious behind it.
"However, early indications are pointing towards a computer glitch with only a small number of votes originating from individuals in EBLEX."
Meanwhile, meatinfo's own poll, which has not been sabotaged, is currently showing 54% in favour of adopting the Red Tractor, with 45% against, and 1% unsure.