Richard Braine entered a public row with the party's ruling national executive committee (NEC) after he called for the cancellation of the conference, which is due to start in Newport on Thursday.
Party chairman Kirstan Herriot wrote to members criticising Mr Braine over his "regrettable decision not to attend our own conference due to low ticket sales".
"Both I and the NEC believe it is a complete insult to the membership to attempt to cancel conference because of a potentially low turn out," she wrote.
"It is also a particular affront to hard-working regional, county and branch officers who have worked hard in encouraging members to attend conference to hear Richard lay out his vision for the future of Ukip. It is therefore a particular shame that he has decided not to do this."
Ms Herriot said the conference would go ahead and Mr Braine would be welcome to take the stage "as leader of our great party" if he has a change of heart.
Mr Batten had been barred from standing again in the leadership contest by the party's national executive committee.
His leadership had become embroiled in controversy after taking on English Defence League founder Tommy Robinson as an adviser.
But the party has struggled to maintain support since its former firebrand leader Nigel Farage resigned as leader.
In 2018 he quit the party entirely, saying it had become unrecognisable because of a "fixation" with anti-Muslim policies.