The investigation followed a referral from sharemarket operator NZX.
A spokeswoman for the Super Fund said the fund had not been contacted by the FMA in relation to the Milford investigation.
"We will be watching the outcome of the investigation closely," she said.
News of the probe comes as the Super Fund searches for an external fund manager to take over the $260 million active equities mandate previously managed by AMP.
AMP's mandate was terminated in November when the Australasian financial services provider made sweeping changes to its New Zealand funds management business.
Auckland's Devon Funds Management also has an equities management mandate with the Super Fund.
On Monday, Milford managing director Anthony Quirk said the company and the trader concerned were "co-operating fully with the FMA".
Quirk said the investigation did not have implications for client funds and had no impact on day-to-day operations at the company.
It is understood confidentiality agreements with the FMA prevent the firm making any further comment.
Market manipulation involves deliberate attempts to interfere with the market to create artificial, false or misleading appearances in supply, demand or the price of securities.
It has been a key focus of the FMA since the regulator was set up in 2011 to replace the Securities Commission, which was widely viewed as ineffective.
Under the Financial Markets Conduct Act, an individual convicted of market manipulation can be jailed or fined up to $500,000, while a company can face a fine of up to $2.5 million.