The SPFL says it received a voting slip from Dundee on their ballot to curtail the lower leagues, but only after the club emailed to say their vote should not be considered as cast.
A slip signed by the club's managing director John Nelms rejecting the proposal has been seen by BBC Scotland.
And in a letter to clubs, SPFL chairman Murdoch MacLennan said in discussions with Dundee, the club's "unequivocal" view was they had not yet voted.
They have 28 days to cast their ballot.
Whichever way the Dens Park club votes will be decisive because the plans need the backing of eight of the 10 Scottish Championship clubs, and only seven of the nine who have taken part have done thus far.
Premiership clubs and those in League One and Two have voted in favour by the required 75% majority.
MacLennan says the league wants to correct "misinformation" which is "damaging" to Scottish football.
He said: "It has been suggested that all Ladbrokes Championship club votes were cast on Friday night.
"One Ladbrokes Championship club attempted to submit a voting slip, which did not reach the SPFL until late that evening. Earlier, at 6pm on Friday, that club had confirmed in writing to the SPFL that any attempted vote from that club should not be considered as cast.
"We have had a number of conversations with the chairman of that club over the weekend, in which he reiterated that his club had not yet voted on the SPFL resolution."
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The SPFL also reiterated its call to Rangers to produce the evidence they claim throws into question the league body's handling of the ballot.
The Ibrox club want SPFL chief executive Neil Doncaster and legal adviser Rod McKenzie removed while an investigation is held.
MacLennan says he wrote to Rangers interim chairman Douglas Park asking for proof of their allegations but has not yet received a reply.
He added: "It is difficult to understand why Mr Park should not wish to share this alleged material with me.
"I am entirely satisfied, based on all the information at my disposal, that the SPFL and its executives and legal advisers have acted wholly properly at every stage in this process."
The league has reiterated its position that prize money cannot be distributed without final placing being confirmed, which some clubs dispute.
Rangers, backed by Hearts and Inverness Caledonian Thistle, tabled their own resolution asking for funds to be forwarded to all clubs but without declaring the leagues. However, that was dismissed as "ineffective" on Friday by the SPFL board.
That led to a rebuke from the club, who said they "sought assistance from the SPFL executive on several occasions" before submitting their proposal.
But the league disputes this and criticised Rangers managing director Stewart Robertson, who sits on the board, saying he was "content" with the discussion on their proposal at the time.