Today's agreement excludes the employee, who is still facing "enforcement processes" from the FMA.
Asked whether the employee was expected to return to Milford, Quirk said: "Obviously the process has got to work its way through."
He said Milford had only lost a "handful" of wholesale and retail clients as a result of the FMA investigation.
"We're putting our hand up and acknowledging we could have done better in this area," Quirk said. "We're a high quality business across all aspects of what we do and that's why we've got such a high quality and loyal client base."
The trading conduct, according to the FMA, was likely to have created the false or misleading appearance of the extent of active trading or the supply demand, price or value of the relevant stocks.
"The FMA also concluded that the Milford Board failed to ensure that there was the requisite degree of monitoring of the trading activity," the regulator said this morning.
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"As Milford is the relevant trader's employer, the FMA considers that Milford is liable for the trader's alleged breaches of the Act," the regulator said.
In addition to Quirk and Brian Gaynor, a Business Herald columnist, Milford's directors are Andrew Cross, Lester Gray, Bryce Marsden and Richard Somerville.
FMA chief executive Rob Everett said the regulator would not comment on the trading activity in question, including the securities involved in the alleged market manipulation.
"We have to respect the individual's rights to a fair process," Everett said.
He said the Milford agreement was "the most sizeable settlement of this nature" that the FMA had reached since its establishment in 2011.
"I believe this is a wake-up call for Milford and the industry," Everett said.
"As we investigated the activity here, we the FMA were not happy with what we found in terms of management oversight and trading within Milford."
He said the regulator wanted to "raise the bar" around management oversight in the industry.
"Boards need to ensure themselves that management have adequate reporting processes and checks in place to ensure they have visibility into what happens within their organisations."
The FMA said Milford denies liability for any alleged breaches but that the pair reached a deal which "resolves the issues" with the regulator.
Under the deal, Milford will pay the FMA $1.1 million and a further $400,000 to contribute to the cost of the FMA's probe.
It will also move to implement improvements its trading systems and controls.
"Milford and its board accept responsibility for the inadequate oversight and control of the trading conduct which was under investigation, and the failure to identify and monitor this activity, or to assess whether the activity was appropriate.
Milford has carried out a thorough review of its systems and processes and has undertaken a programme of improvement for its trading systems and controls. Milford appointed PwC to review its governance, risk and compliance capability and to provide recommendations. That review has now been completed and provided to the FMA. Milford undertakes to complete a further external review following implementation of PwC's recommendations," the FMA said.
Quirk said the company was pleased the investigation had been concluded. He said it was important to note that, as stated by the FMA, the investigation had not related to the security of client funds or assets.
"This rules a line under the investigation from Milford's perspective and we are now looking forward to focusing completely on continuing to deliver returns to our investors," Quirk said.
"We understand the role that the regulator has in ensuring that monitoring systems are at the highest international standards. We acknowledge that ours needed improvement in specific areas and this has been done."
Read the full FMA - Milford Asset settlement here:
