The UK Independence Party MEP blogged about the "very similar pattern" between a 1942 Nazi draft plan for harmonising European governance and currencies after a total Nazi victory, and the European Commission.
The comments by the London member follow former London mayor Boris Johnson's comparison between failed plans for European empires. Johnson attracted criticism for likening the EU's aims to those of Adolf Hitler.
The Nazis drew up the "basic plan" for the EU decades before it was actually established, Batten has claimed.
Batten suggested Johnson had actually underplayed the connections between the EU and the Nazis, and that the EU had "closer links" with the fascists than many realised.
He said the first President of the European Commission had been "a member of several nominally Nazi professional organisations" and served in Adolf Hitler's army.
"In 1942 when the Germans still thought they were going to win the war they produced a report entitled the Europaische Wirtschafts Gemeinschaft - which translates as the European Economic Community," he wrote in a post on his blog.
"The report contained sections on agriculture, industry, employment, transport, trade, economic agreements, and currency. It proposed the 'harmonisation' of European currencies and a harmonised currency system.
"If this all sounds all very familiar it is because the basic plan for the European Economic Community of 1942 was very similar to the actual European Economic Community that came into existence in 1957 under the treaty of Rome."
Batten said: "What emerged as the European Economic Community in 1957 was created by the kind of people who would have run Europe's economies if Germany had won the war, and their plans followed a very similar pattern."
On Monday, reaction to his remarks was swift, with UK Tory MEP Charles Tannock telling this website, "This is a burlesque statement and bears no relation to the truth. The EU was founded precisely to avoid the horrors of another major war on our continent."
Tannock added, "The EU is a voluntary association of democratic countries prepared to pool some sovereignty for the common collective good and is as far removed as one can imagine from the totalitarian genocidal attempts by Hitler to force Europe under the Nazi thumb. It is an unworthy statement by any UK politician who has the minimal knowledge of 20th Century European history."
Denis MacShane, a former Europe Minister in the UK who is campaigning for Britain to stay in the EU, said, "The desperate efforts by batty Europhobes to link Hitler with EU shows they know no history. They might as well say Genghis Khan or Attila the Hun were forefathers of EU. The fact is that
European integration was a response to fascism and Stalinism and those who want to return the UK to pre-war isolationism are bonkers."
Former ALDE MEP Andrew Duff commented, "It is unethical to relativise the Nazi regime - trying to explain it by putting the Third Reich into a normal historical context.
"The post-war moves to European integration were the antithesis of fascism. Instead of forcing citizens to serve the state, the European Community aims to serve its citizens. In that sense, the EU is the prize of victory over Nazism. Batten finds himself unable to disguise his true colours."
Labour MP Chuka Umunna said the Leave camp was deploying "crackpot conspiracy theories" in lieu of explaining what Britain's role in the world would be outside the EU.
"This is yet another crackpot conspiracy theory from the Brexiteer brigade who want to leave the EU at all costs," he said.
A UKIP spokesperson said, "We do not wish to comment."