Nikko NZ, formerly Tyndall Investment Management, rebranded under its Tokyo-based parent company's name last year and has more than $4 billion in assets under management.
Lynn said one of the benefits of being part of a global company was the resources that could be put into risk management and compliance around trading best practice.
"We're very confident that our investors are getting absolutely pure investment returns and are benefiting from the market as they should. What we don't want to see is the market disturbed at all by inappropriate practices."
Milford managing director Anthony Quirk last week said the company and employee concerned were co-operating with the FMA.
The investigation had no implications for client funds and would not impact day-to-day operations, Quirk said.
Meanwhile, Lynn said there could be some life left in the equity bull run, which has seen stock markets rally for almost six years.
"We're clearly seeing a slowdown in the growth of that bull market but it's likely to perpetuate for a little bit longer," he said. "The reality is interest rates globally are so low, which provides stimulus to equity markets."
