Two Royal Navy patrol vessels – HMS Severn and HMS Tamar – were also at the scene, after being sent by the UK government on Wednesday night.
Both vessels stayed clear of the main flotilla, with HMS Severn near Corbière and HMS Tamar in St Aubin's Bay.
UK Prime Minister Boris Johnson spoke to Chief Minister John Le Fondré, Deputy Chief Minister Lyndon Farnham and External Relations Minister Ian Gorst on Thursday morning to pledge his 'unequivocal support' to the Island.
In a statement released on Thursday evening, Mr Johnson said: 'We are pleased that French fishing boats have now left the vicinity of Jersey. Given the situation is resolved for now, the Royal Navy offshore patrol vessels will prepare to return to port in the UK. We remain on standby to provide any further assistance Jersey requests.
'The Trade and Co-operation Agreement brought in changes to fishing arrangements between the UK and the EU. Jersey authorities have a right to regulate fisheries in their waters under this agreement and we support them in exercising those rights.
'We will work with Jersey to support the discussions underway with the European Commission.'
The protest comes days after the French Minister for the Sea threatened that the country could cut Jersey's power supply unless the licensing regime was changed.
Up to 60 vessels took part in the protest off Jersey's south coast. Earlier on Thursday morning they entered the Harbour but later left to allow commercial vessels to depart.
French fishing boats are now steaming towards the harbour mouth. Rumours of a potential blockade being spoken about over marine radio pic.twitter.com/kjAjnLnw0c— jepnews (@JEPnews) May 6, 2021
Assistant Environment Minister Gregory Guida and other government officials met French fishermen at around 10.30am, following a request from the crews.
In order to comply with Jersey’s Covid guidelines, the government representatives used the Norman Le Brocq Fisheries boat, while the French fishermen were onboard another vessel.
Senator Le Fondré said: 'The French fishermen protested peacefully and respectfully, and were able to set out their concerns directly to government representatives.
'We recognise that there have been challenges in the implementation of the new trade agreement. Speaking directly to the fishermen has enabled both parties to better understand how those challenges will be addressed, and we are proposing the establishment of a forum which will enable the Government of Jersey to continue to engage with all fishermen in the region openly and constructively.
'I’d like to thank Deputy Guida and all the other parties whose work has enabled the French fishermen to leave Jersey knowing that they had been listened to, and that a step has been taken towards resolving the issues that have arisen during the move to the new trade agreement.'
At around 1pm, the French vessels left Jersey.
External Relations Minister Ian Gorst, said: 'We are meeting with French fishing leaders to listen to their concerns regarding fishing rights. There are continuing extensive political and operational efforts with both our local fishing community and French fishing associations, their regional representatives in France, and both the UK and French governments, in order to resolve the current dispute and resume previous good relations.'
The Commodore Goodwill freight ship, which was due to leave the Harbour this morning, eventually left port four hours after it was scheduled to depart.
Elwyn Dop, Condor Ferries’ operations director, said: ‘Due to the disruption this morning in St Helier, the departure of our freight ship, Commodore Goodwill, had to be delayed until safe passage could be arranged.
'She arrived in Jersey at 4.30am, discharged her cargo as usual before leaving for Guernsey at 11.15am, just over four hours behind schedule. Timings for today and tomorrow have therefore been revised to accommodate the delay.
'Disruption was minimal with no impact on the freight supply chain, which brings in 95% of the essential food, medical and other goods into the Channel Islands.
'We expect our freight and passenger vessel, Commodore Clipper, to operate to Jersey this afternoon from Portsmouth and Guernsey as normal.’
In a tweet, Paul Luxon, Condor's chief executive, said: 'Sadly she is trapped, we tried to bring her in earlier so in - discharge, load - out, and on her way, but in dialogue with Jersey Authorities ‘safety first’ of course.'
Two Jersey boats – the Normandy Trader and Sanderling – also joined the demonstration.
Jersey fisherman Josh Dearing described the scene as 'like an invasion', with the French fleet mostly made up of 'big French trawlers' of 12 metres or more.
The 28-year-old told the PA news agency: 'There were probably about 60 boats. There were a few hand-held flares and smoke flares going off and apparently a few maybe bangers and stuff going off from the French.
'It was quite a sight. It was impressive, I looked from the shore this morning and it was just like a sea of red lights and flares already going off at sea. It was like an invasion.'
Jersey's government yesterday called for an urgent de-escalation of tensions between the Island and France.