The former deputy prime minister and National Party leader has applied to recontest his northern New South Wales seat of New England.
But an eight-member selection committee has reached a deadlock and is unable to unanimously support his candidacy, Sky News reported on Wednesday.
At least two members are holding out, fearing Mr Joyce could have "more skeletons in the closet".
The reluctant members have argued Mr Joyce did not declare his extramarital affair with former staffer Vikki Campion when he filled in his paperwork in 2016.
If the selection committee cannot resolve the impasse, the party's national executive will be forced to step in.