He said: "The heroism and valour shown by the people who went to the rescue of the thousands of troops stranded on the beaches of Dunkirk 70 years ago is a testament to the courage and endeavour of British people.
"Our country should always be grateful to and remember all those who were involved in the evacuation, and our thoughts go to all those who didn't make it home."
The phrase "Dunkirk spirit" is seen as emblematic of British determination and courage in the face of adversity.
As the boats entered Dunkirk they were greeted by a French piper.
Richard Basey, who was among the first to arrive, said the journey across the channel had been ideal.
He said: "It has been excellent. The sea conditions were very kind to us. The wind had dropped completely. We have had a very good crossing."
He said it was important to remember that many died during the war. He said: "We are here to celebrate and remember the losses."
The BBC's Robert Hall said there was a great sense of "family" among those who had taken part in the journey.
The flotilla in Ramsgate, Kent, was cheered by rain-soaked crowds as it set sail for Dunkirk, in north-east France, at 0700 BST.
BBC correspondent Jon Kay was on board the Greta, the oldest of the little ships that brought back hundreds of exhausted men 70 years ago. He said for the last few hours it had felt like he was in 1940.
While on the trip, he was joined by Brian de Mattos whose father Basil was part of the rescue mission.
Mr de Mattos said: "It's a great honour for me to be following in my father's footsteps 70 years later. To see all these little ships is really quite an emotional time.
"My father made many trips in and out of Dunkirk harbour often under fire from the enemy."
The original evacuation took place between 26 May and 4 June 1940, and involved 900 naval and civilian craft which were sent across the Channel under RAF protection.
War veterans were among those on board the flotilla
Among them were a number of smaller vessels including fishing boats pleasure crafts, paddle steamers and lifeboats.
During the evacuation - described by Winston Churchill as a "miracle of deliverance" - the Luftwaffe attacked whenever the weather allowed and at least 5,000 soldiers were killed.
English Heritage historian Paul Pattison said the troops who disembarked at the ports of Dover were given a warm and compassionate welcome.
He said: "They were given a cup of tea, a ham sandwich and clothing where they needed it because they were wet and bedraggled and often blood-stained.
"They were then very quickly put onto trains and dispatched all over the country - away from the danger zone - for a bit of rest and recuperation before they were ready to join their units again."
Ramsgate's Royal Harbour Marina was the reception centre for returning troops and after a weekend of commemorative events in France, the little ships are due to return there on Monday.
Edwin Brown, who was among those rescued in 1940, told the BBC: "They made a hell of a difference because they got us out to the bigger boats where we could get some help from the sailors who couldn't get in because of the depth of the water.
"There isn't a better spirit anywhere because everyone was looking after each other.
More than 300,000 Allied troops were rescued from the Dunkirk beaches
"If you were in trouble and you needed help, it was there. That was the Dunkirk spirit."
The ships were escorted by the Royal Navy frigate HMS Monmouth - the youngest ship in the flotilla - on their eight-hour journey.
Rear Adm Tom Cunningham said it was important for his crew to take part.
He said: "We all have very strong bonds in the maritime community and we recognise... what a sacrifice and what bravery it took for [the small ships] to do it."
A commemorative ceremony is due to be held at the Allied memorial on Dunkirk beach on Saturday. There will be a minute's silence, followed by the national anthems of Britain, the Czech Republic, France and Belgium.
Historians say the evacuation boosted British morale at a crucial point of the war.
World War II expert Nick Hewitt said Dunkirk "bought time" for the Allies, allowing them to regroup and fight another day.
"Without Dunkirk, Britain wouldn't have had an army and it's extremely questionable whether it could have fought the war," he said.
German forces advancing rapidly through Belgium and France forced the
British and French troops back around Dunkirk. A brief halt by the Germans allowed evacuation of troops to begin under "Operation Dynamo".
Evacuation of British troops started on 26 May. Passenger ferries led the rescue convoy from Southampton and Dover. Shelling by German troops forced the ships to take a longer route, to the beaches east of Dunkirk.
Shallow water prevented the big ships getting close to shore so
a convoy of little ships, including pleasure craft, tugs and fishing boats, sailed from the UK on 29 May. Low cloud and burning oil provided cover for troops to escape.
The last British troops were brought out on 2 June. With German forces closing in, only one more night-time evacuation was possible. More than 26,000 French rearguard troops were rescued that night, bringing the total saved to 338,226.
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