The audit also found five instances where the account had become overdrawn, in amounts ranging from $180 to $25,000.
In two instances, deposits were paid out to incorrect accounts then returned by the banks, and in another instance money was paid to the wrong solicitor.
In its penalty decision, the authority said the agency had allowed systemic disorder into its administration systems, leading to a "startling amount of errors".
The lapses carried a serious risk, and it was only a matter of time before a consumer was affected.
It was "merely by an element of good luck" that the errors had not led to severe consequences.
Neil Christie, who resigned as principal officer during the period concerned, was censured and fined $2000.
Colin Richardson, an experienced agent who then took over control of the agency, was reprimanded. It was noted the conduct was outside of his control for most of the relevant period.
The agency was fined $5000.
Agent blamed quake for debt
In another case that went before the Tribunal, a real estate agent who defrauded clients of $25,000 blamed the impact of the Christchurch earthquakes for driving him into debt.
Chairat (Henry) Santipongchai, formerly a top agent for Harcourts in Canterbury, admitted misappropriating money from three clients.
Mr Santipongchai faced four charges of disgraceful conduct before the Real Estate Agents Disciplinary Tribunal.
In one case he misled a restaurant owner who was selling their business into paying $5000 in marketing costs, which he used for his own benefit.
In another, he obtained $20,000 from prospective buyers of the same business, telling them the money would be held in trust until the title had transferred, but immediately used the money for his own purposes.
He also took $499 from the vendor of a motel for advertising, but used the money himself.
Only the restaurant owner has been repaid.
The fourth charge was that he carried out real estate agent's work without a licence.
In a written response to the tribunal, Mr Santipongchai said he was regretful and accepted responsibility, "even though I may have foolishly thought I was doing the right thing at the time."
He said he was bankrupted by the IRD in 2013 after falling behind in debt repayments due to the impact of the Christchurch earthquake on his business.
Mr Santipongchai had voluntarily surrendered his licence after the complaints were laid, and said he intended to undertake missionary work in Thailand.
He wanted to devote his time to helping people do the right thing and building churches.
"I am trying to pick up the pieces put them together into a better me and a better life," he said.
The tribunal said his conduct was serious and he should be firmly penalised, however a fine or order for compensation would be futile because of his bankruptcy.
It ordered his licence to be cancelled.