Bayleys has admitted its conduct breached the Commerce Act and has agreed to settlement terms.
None of the other agencies have settled.
Agents allegedly agreed vendors - not the agencies - would have to pay Trade Me listing fees, which went up under a new pricing model in 2013.
The commission filed proceedings in the Auckland High Court for alleged price fixing and anti-competitive behaviour by national and regional real estate agencies, a company owned by a number of national real estate agencies, and three individuals.
It also issued warnings to an additional eight agencies for their alleged role in the conduct.
Mr Cosgrove expressed concern at the allegations.
"It appears that people buying and selling properties have paid more than they should have, if the commission's case is upheld. If the case succeeds, those companies should immediately refund those monies," he said.
Suzanne Chetwin, Consumers Institute chief executive, has expressed concern for parties involved in the massive house selling industry, with an annual $1.2 billion turnover.
A spokesman for Bayleys said the matter was before the courts and the company was unable to comment further.
A spokeswoman for Barfoot & Thompson said a press release would be issued. No release had been received by 8.30pm yesterday.
"There won't be any other comments, as this matter is before the courts," she said.
Ray White NZ chief executive Carey Smith said Ray White had not agreed to any settlement.
"We will review our position as we gain further understanding as to the detail in proceedings that have now been filed," he said.
A spokeswoman for LJ Hooker said it would not comment as the matter was before the court.
A statement from Monarch Real Estate said its directors were aware of the allegations by the commission.
"The allegations relate to efforts made in 2013 to resist a massive increase in Trade Me listing fees that would apply for home sellers," the statement said.
"On receiving advice of Trade Me's fee increases, the main focus of the actions taken was to serve the best interests of clients and consumers. Competitiveness was improved as a result, and costs avoided."
The chief executive of Success Realty, Ross Stanway, referred any comment about the commission to Bayleys. Success Realty trades under the Bayleys banner.
Steve Allen, the principal officer at Manawatu 1994, which trades under the LJ Hooker banner, said he could not comment as it was an ongoing investigation.
What's alleged
• Real estate agencies paid a monthly subscription to advertise their listings on Trade Me.
• In 2013, Trade Me announced fee changes for real estate agents listing properties.
• All real estate agents were shifted from a capped monthly subscription plan to a fixed fee-per-listing structure.
• Barfoot & Thompson, Harcourts, LJ Hooker, Ray White and Bayleys are alleged to have breached the Commerce Act with a planned industry response.
• They allegedly agreed among themselves to pass on increased Trade Me fees to vendors.