Brutal weather conditions hampered search efforts, and cast doubt on the mens' ability to survive at sea.
The missing mens' families were devastated, police said, as were staff at the Lyttelton-based company operating the boat.
"It's a difficult time for both the company, and obviously, more so for the families," said Andrew Stark, chief executive of Ocean Fisheries and Stark Bros.
The boat went missing 12 nautical miles (22km) from the Rakaia River mouth, south of Christchurch.
Conditions at sea were rough, with winds blowing up to 40 knots (74km/h), Mr Stark said.
The searchers had to battle 3 metre swells and choppy waters, he said.
"It's not an easy search from the air or from the sea."
The three men on board were familiar with the Jubilee, Mr Stark said.
"They're all experienced with the boat," he said.
One of the men on board the Jubilee was believed to have family in Motueka.
Family members have asked for privacy.
The air and sea search covered about 170 sq km.
An aerial search spotted debris from the Jubilee, Inspector Craig McKay of Canterbury Police said.
A boat taking part in the search then recovered an empty liferaft, confirmed as belonging to the Jubilee.
Fishing bins and documents were also recovered, as was oil and other fluids.
An underwater search would begin, in the hopes of recovering the boat.
The boat's last known location was in a spot where the waters were up to 45m deep, Mr McKay said.
Two Coastguard boats, three commercial vessels, the Westpac Rescue Helicopter and an aeroplane joined the search.
Coastguard Southern Region said the rescue boat Blue Arrow Rescue went to the Rakaia River mouth area "in difficult conditions" to search for survivors.
Coastguard Canterbury also joined the search, heading south from Pigeon Bay near Akaroa.The Jubilee was launched in January 2008.
At that time, Stark Bros said the boat would fish the "varied conditions and fishing grounds" off the South Island east coast, in seas from 10m to 500m deep.
