Warminger, through his lawyer, has denied the allegations and said he will defend the case.
"When the facts are traversed in court the public will be able to draw its own conclusions on both the FMA and this particular claim," defence lawyer Marc Corlett said in a written statement.
"The fact that the FMA asserts something does not of course make it so and we fully expect that fair-minded people will wait until the court process is complete before drawing any conclusions about Mr Warminger's trading."
A statement from the FMA alleges Warminger's trading fell into the three categories:
• placing small trades directly on market in one direction, followed by large off-market trades in the opposite direction;
• trading that manipulates the closing price; and
• trading conducted in order to set the price, rather than for a genuine commercial purpose.
In response to this, Corlett said that it was "a matter for interpretation, firstly whether the activity was as suggested; and secondly whether, even if that were so, (which is denied) it would constitute market manipulation."
FMA director of enforcement and investigations Belinda Moffat said the issues in the case were "of significant importance to New Zealand's secondary markets and the FMA's focus on ensuring that our markets are seen as fair and transparent places to do business."