Milford has held the external management mandate since 2009.
The funds would be managed internally in the interim, the Super Fund said.
"We appreciate that the FMA has rigorous processes to go through and that market investigations can be complex and take time," a Super Fund spokeswoman said.
"Given the passage of time since the investigation was confirmed, however, we have decided to put the mandate on hold until the investigation is complete."
Milford said it was surprised by the Super Fund's decision to suspend the mandate.
"We have not commented on the specifics of the investigation because we respect the due process of the FMA investigation and are bound by a confidentiality order imposed by the FMA," said managing director Anthony Quirk.
"We will continue to refrain from any comment that could be seen as undermining the investigation process or pre-empting the outcome.
"In the meantime we look forward to completion of the investigation and release of any findings."
In February Milford confirmed that an "individual trader" employed by the company was being investigated over "certain specific trades".
"Milford and the trader concerned are co-operating fully with the FMA," Quirk said at the time.
Milford has more than $3 billion in assets under management, including KiwiSaver funds.
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