Mr McDonnell, who is running Jeremy Corbyn’s campaign to retain Labour’s top job, accused Mr Smith of “flip-flopping” in the wake of reports some MPs intended to trigger a “semi-split” in the party.
“If he continues to refuse to denounce those calling for a split, then members will think he is simply trying to scaremonger them to vote for him by his talking up of threats from a minority of MPs supporting his campaign who are plotting to split our party in Tory newspapers, while at the same time refusing to denounce them.
“And it’ll be hard for anyone to tell how much Owen truly is opposed to a split, and how much he is giving tacit support to those plotters in a hope it helps his campaign.
“Owen Smith therefore needs to immediately distance himself from those people saying they want a split, which is causing huge damage to our party at this time. Anything short of this will make him the ‘disunity candidate’,” Mr McDonnell said.
The comments came as leading Smith supporter Kate Green wrote to the chair of the pro-Corbyn Momentum group seeking to organise a leadership debate.
Ms Green, who chairs Mr Smith’s campaign, accused Mr Corbyn of refusing to take part in a planned debate on Channel Four this week.
The MP said she was writing to “seek an assurance that Jeremy does not intend to pull out of the remaining media debates that have been scheduled for the rest of the campaign”.
As the bitter tussle continued, shadow home secretary Andy Burnham claimed he would be leader of the Labour Party if leadership election rules had not been reformed by Ed Miliband.
Meanwhile, Mr Corbyn has called for business reform after the collapse of BHS.
The Labour leader told The Observer he wants it to be mandatory for employers with more than 250 staff to bargain collectively with unions.
Mr Corbyn also criticised the former owner of BHS Sir Philip Green, saying he had “asset stripped the company” and “left the Government to pick up the pieces”.
And Mr Smith demanded reform of the honours system following reports of who would be included on David Cameron’s resignation list.