Inverness chief executive Scot Gardiner says Dundee had informed them they had voted against the SPFL's resolution to end the season in three divisions and potentially the Premiership.
The Scottish league's board met on Friday to consider the responses to its proposals put forward on Wednesday, needing nine supporting votes from the top flight and eight from the second tier.
The Premiership reached its requirement, but only seven votes came in favour from the Championship, with Partick Thistle and Inverness voting against and "a technical question mark over the competence of Dundee's no vote", Sky Sports News has been told.
In response to the technicality over the Dundee vote, Gardiner said that Inverness, Partick Thistle and Dundee were part of a WhatsApp group and all said that they would vote no to the SPFL resolution.
It was claimed that Dundee posted an image of a signed "no" voting paper on Friday, shortly before the Dundee secretary sent a message saying they had submitted that vote.
Gardiner said when the SPFL released the voting standings on Friday evening, they realised that Dundee were the issue.
Following the release, Gardiner then received a text message from the Dundee secretary saying "you have my solemn word that the vote was submitted".
He claims that Partick Thistle chairman Jacqui Low text the group to tell Dundee to submit the vote again, but that the Dundee secretary said he had been told to hold off resubmitting the vote.
Dundee had earlier suggested they would vote against the plan, stating on Friday "the current proposal condemns clubs to be financially worse off than they already are as we sit here today".
The plans would see the immediate curtailment of the bottom-three league seasons plus the right for the SPFL board to decide the Premiership on a point-per-game basis, if the coronavirus prevents its resumption in the short-term.
This would see Celtic be declared champions and bottom side Hearts, who voted against, relegated to the Championship, with Dundee's fierce rivals Dundee United promoted to the top tier.