The row centres on Scottish Labour suspending a local consultation in Falkirk on whether an all-woman shortlist should be introduced for the seat amid fears the survey was biased and flawed. Local members responded by approving a resolution slamming party headquarters for acting "in isolation" and tarnishing the process.
Joyce's conviction for assault last year means Labour are looking to select a new candidate in Falkirk for the 2015 General Election.
The three contenders are: former council leader Linda Gow; Gregor Poynton, the UK political director of communications firm Blue State Digital; and trades union activist, Karie Murphy.
Unite, Labour's biggest trades union backer, is supporting Murphy and signed up dozens of new members to the local party last year.
The union also paid for the postage on a "consultative survey" on whether an all-woman shortlist should be used for the safe seat, a decision that would benefit Murphy.
But the Scottish Labour Party (SLP) scrapped the Unite-funded consultation after it emerged only some local members received a copy.
The question in the survey also raised eyebrows: "Do you agree that Falkirk would benefit from an All-Woman Shortlist for the Westminster selection?"
The "do you agree" formula is widely seen as biased and was ditched by the SNP Government as its preferred option for the independence referendum.
After the survey was binned, a troubleshooter from the UK party was parachuted in to help run the selection process.
However, the decision to halt the survey has enraged the local party, which passed a resolution condemning Scottish Labour.
The resolution noted: "We condemn this blatant disregard for the democratic decision taken by Falkirk West CLP [Constituency Labour Party].
"The SLP has acted in isolation and rejected inclusiveness – a priority that would have ensured the process retained the trust and confidence of our members.
"It is our view the SLP has tarnished this process, exposing us to the manipulation of the media and the manipulations of individuals for personal gain."
However, a senior Labour source said the resolution was a case of "sour grapes" from the people behind the flawed consultation. "The individuals who messed up the survey are now complaining about the Scottish party stepping in to sort it out."
A second Labour source said the "key issue" in the Falkirk race was whether the new members signed up by Unite would get a vote at the selection meeting.
SNP MSP John Wilson said: "It is clear that a civil war has broken out inside the Labour party in Falkirk. After all the trouble involving Eric Joyce, the people of Falkirk deserve better than this sort of nonsense."
A Scottish Labour spokesman said: "We will ensure that all selection procedures are followed correctly to allow the members in Falkirk to select the best possible candidate to represent their community."