Thomson indicated her client wanted a jury trial.
The SFO said earlier this month that Jane Rose was also involved for some time in the alleged offending, which according to the agency took place between June 2005 and December 2012.
A SFO spokeswoman said that the Roses, both 42, were husband and wife - at least at the time of alleged offending.
Jane Rose, represented in court this morning by Shane Kilian, turned up separately to her co-accused and also entered not-guilty pleas.
Kilian said his client also wanted a jury trial and the pair are next due to come to court on November 26.
MRP chief financial officer William Meek said when the charges were laid that they related to a historic matter and that any financial impact was absorbed into past accounts.
The company has changed its procurement and inventory management process to minimise the "risk of recurrence".
Any decisions around recovery options would be made by the company following the SFO's court action, Meek said earlier this month.