The nine-strong Labour group was suspended last week for forming a coalition with the Conservatives.
Alan Massie said party's executive committee needed more local people.
Scottish leader Kezia Dugdale said the SEC represented the party well.
The Labour group signed a deal with the Conservative and independent groups last Wednesday, allowing them to out-vote the SNP - who finished as the largest party on the council in the recent election.
Scottish Labour's executive committee (SEC) ordered its councillors to stand down from the coalition.
The councillors were suspended after the deadline for standing down passed - meaning there were no councillors in Aberdeen representing Labour.
BBC Scotland asked property developer Mr Massie if he still backed Ms Dugdale.
He said: "I think that's an unfair question, I think the short answer is yes, but I have no confidence in the SEC, and I think that the leadership needs to address that.
"So Kezia, in terms of overall confidence in the party, I have confidence in it, but the SEC I have no confidence on that.
"We need to break down all this heavy central belt membership on that, and we need to get more people locally on all these SEC meetings to deal with the local party."
However Ms Dugdale said the committee was made up to reflect the party across Scotland.
She said: "The Scottish Executive Committee represents every aspect of the Scottish Labour Party, our roots in the trade union movement, elected representatives from different constituency parties, all across Scotland, it is what the Labour party represents, working people.
"The body of people on the SEC that took that decision are from that broad mix of the Labour movement."
The local elections saw the SNP become the biggest party in Aberdeen after returning 19 councillors, with the Conservatives on 11 and Labour on nine.
Four Liberal Democrats were also returned, and two independents.
Lib Dem councillor Jennifer Stewart has now left the party group to become an independent.
The council had been run by a Labour-Conservative coalition since 2012.
An Aberdeen businessman who is one of Scottish Labour's biggest financial backers has said he will not give the party any more money during the general election because of its suspension of councillors in the city.