The Amalgamated Workers' Union said dozens of companies had complained about being owed money by the commission, The Press reported today.
Action Demolition contracts manager Paul Munro said his company was owed more than $300,000 by the EQC and was considering legal action.
Union secretary Calvin Fisher said although there had been issues with some companies issuing false invoicing, the commission appeared to be overwhelmed by the amount of work it was processing.
Employers were submitting as many as 35 invoices a week to the commission, he said.
Mr Key said today that tradespeople had raised the issue with him and he was looking into the complaints.
The EQC had a lot of claims to deal with and was paying its bills, but it appeared there were discrepancies, Mr Key said.
"But generally we have said, 'Just err on the side of getting the bills paid'," he told Newstalk ZB.
"You're talking about a lot of tradespeople keeping the economy going down there and we need to keep that work going."
A commission spokesman said if invoices were in order, payments were usually made within about 21 days.
"If, however, EQC has an issue with an invoice, it is contacting the contractor to discuss and explain what is missing or required on that invoice.
"Some contractors are not willing to comply with requests from EQC regarding their invoicing, and subsequently payment is delayed."
The commission was examining all claims for potential fraud, with 344,000 claims received so far from householders and contractors.
