The incident occurred at 5am on Sunday about 12 nautical miles off the coast near Rakaia, the commission said.
A team of two investigators have begun gathering information and working with search authorities and the fishing company on an investigation plan.
The plan includes options for inspecting the sunken vessel.
The commission said the aim was to find out what has happened and why in order to prevent a similar situation happening again.
READ MORE: Search for missing fishermen continues today
Two Coastguard crew members, a representative from Canterbury search and rescue and five dive squad members were making their way to the location this morning, he said.
The boat was sitting on the seabed about 40m below the surface - and it would depend on weather and sea conditions if divers would be sent in as the tide drops, he said.
"While the wind has dropped there are still 1.5m southerly swells in the area," Mr McKay said.
"The dive squad will assess the conditions when they reach the site and hope to be able to deploy their radial sonar to verify whether the item of interest is the FV Jubilee and it's orientation to the seabed.
"If the item is consistent with that of the FV Jubilee the additional data will be assessed along with the weather conditions and sea state before putting any divers in the water."
The recovery was an ongoing process, he said.
It was too early to say whether the item of interest was the FV Jubilee but its location was consistent with the boat's last known position.
Police would provide an update later today, a spokeswoman said.
