The vote was spotted by Iron-Bru.net messageboard users, who highlighted concern of potential matchrigging.
Prompted by Iron fans, the Football League promised to look into the matter.
But the Cods insist that they will be going out to try and win Saturday's game at Blunder Park, a result which would ironically guarantee United promotion.
Cods spokesperson David Smith told the Scunthorpe Telegraph: "Being a professional club, we are not into the business of that sort of thing.
"It was probably meant light-heartedly. Come Saturday the players will be 100 per cent ready to play Southend United, regardless of what the result would mean to our local rivals.
"I don't know who put it on there but it is not on there anymore."
United's general manager Jamie Hammond added: "I have been in touch with Grimsby Town's chief executive and he has assured me that they will be going out to win the game on Saturday.
"He is also investigating how the poll came to be on the website."