Lifeboats and fellow fishermen returned to St Helier's harbour after around 12 hours of searching.
Lifeboats, planes, helicopters and other fishing vessels combed the water for more than 12 hours after a freight ship and a fishing boat crashed. in the early hours of Thursday 8 December.
Jersey Coastguard has confirmed that Condor Ferries' freighter, the Commodore Goodwill, and a Jersey-registered fishing vessel collided at around 5:30am.
A spokesperson said: "Debris from the fishing boat is in the sea and the vessel is believed to have sunk".
The fishing boat's skipper, Michael 'Mick' Michieli, and two members of his crew were on board the L’Ecume II at the time of the collision.
Rescue services - including lifeboats from Jersey and Guernsey's lifeboats, French naval aircraft and two French rescue helicopters - are taking part in the ongoing search.
Sources have told ITV News that five Jersey fishing boats have joined the search.
Condor Ferries confirmed their freight vessel was "involved in an incident" while sailing from Guernsey to Jersey. CEO John Napton said:
"The ship departed Guernsey for Jersey at 04:41 this morning and the incident occurred at around 05:30. She is carrying five passengers, 24 crew, and the master remains in full command of the vessel."
Scuff marks were visible on the Commodore Goodwill as it arrived back in St Helier's harbour.
Ship tracking service, MarineTraffic, shows a number of fishing boats, as well as the Goodwill, were in the area at the time.
The Goodwill has now docked in Elizabeth Harbour and Jersey Coastguard is continuing to coordinate the response.
Freight driver, Richard Henry was onboard the Commodore Goodwill when the boats collided. He heard five long blasts on the ship's horn and then a 'big bang'.
He said the whole boat tilted when the impact occurred and then he saw the fishing boat drift away, as the Condor sailed past:
Eyewitness Richard Henry described what he saw at the time of the crash. The Coastguard later confirmed the fishing boat was a Jersey vessel.
Mr Henry praised Condor's response to the crisis, saying the Captain kept all onboard informed. He said within minutes, the crew were dressed in their rescue gear and had launched the onboard lifeboats.
He said: "At about 6:10am we saw four or five lifeboats, and two helicopters flying around with big searchlights on.
"Even when the Goodwill boat turned around they had four or five big spotlights out. They were doing everything they could to find the people overboard."
Mr Henry says everyone was concerned for the welfare of the fishing crew.
Condor Ferries says it notified the authorities, the Goodwill assisted in the search effort and the company will "fully comply with any investigation into the incident".
Don Thompson, the President of the Jersey Fishermen's Association says it is a "rapidly changing situation" and while they are still "hoping for the best", they are "preparing for the worst".
Reading a statement on behalf of Jersey Coastguard, the island's harbourmaster Bill Sadler gave an update on the search effort.
Jersey's Harbourmaster, Bill Sadler, gave an update on behalf of the Coastguard at 2:30pm on Thursday 8 December.
He said: "The vessel is believed to have sunk in approximately 40 metres of water, which requires specialist divers.
"An offshore construction vessel currently working on the St Brieuc wind farm project will be coming with one of its remote-operated vehicles to confirm the location of the boat.
"Jersey Coastguard is continuing to coordinate the response, in conjunction with the States of Jersey Police, Government of Jersey, and other agencies."
At 5pm on Thursday 8 December, the Coastguard announced its search and rescue operation would be suspended for the evening, but resume in the early hours of tomorrow:
"Jersey Coastguard is suspending overnight the search and rescue operation on the west coast of Jersey.
"Search and rescue services will regroup before first light tomorrow to consider the findings of the search by the remote operation vehicle (the uncrewed underwater craft) before deciding how to proceed."
A 12-hour air-sea search took place off Jersey's northwest coast for the three fishermen who have been missing since Thursday morning.
An exclusion zone has been set up in the area surrounding where the crash happened, with commercial shipping vessels rerouted eastbound to avoid the area.
Anyone in Jersey who found debris from the L’Ecume II is being asked to report it to the Coastguard on 01534 447705.
Condor Ferries says: "This is a very difficult situation and our thoughts are with the families and loved ones of these fellow seafarers as we all try to come to terms with what has happened."