The fishing boat was found sunk off the Canterbury coast after its crew sent out a distress signal from a brutal storm on October 18.
The boat's three crew - fishermen Jared Reese Husband, 47, of Timaru, Paul Russell Bennett, 35, of Motueka, and Terry Donald Booth, 55, of Nelson - are presumed dead.
Members on board the diving support vessel - HMNZS Manawanui - performed a "Piping of the side" when the men were recovered on Monday, Mr Simmonds said.
The wreck is 40m underwater and the dive team could only conduct a "fixed number" of dives throughout the day, he said.
Weather conditions have prevented more dives from taking place today but the search should resume on Wednesday, he said.
"Unfortunately the weather has deteriorated overnight and no diving will take place today.
"However weather permitting the intention is...to return to site tomorrow to complete the search of the wreck of the FV Jubilee.
"Canterbury Police would like to thank the Royal New Zealand Navy for their ongoing assistance during SAR recovery phase the focus of which, if possible, is to locate and return the missing men to their families."
Police and Transport Accident Investigation Commission inquiries into the sinking are ongoing.
An update on the search would be available on Wednesday.