The new foreign secretary made the claim following a meeting on Monday with his German counterpart Heiko Mass.
Posting on Twitter, Mr Hunt said the pair held an “excellent discussion” about the “unintended geopolitical consequences” of the UK leaving the EU without a divorce agreement.
He added: “Only person rejoicing would be Putin.”
In response to the foreign secretary’s comment about the Russian president, Tory Remainer Ed Vaizey pointedly asked: “So why do people suggest that no deal would be better than a bad deal?”
The government – and Theresa May herself – have routinely claimed “no deal is better than a bad deal”.
Mr Hunt had earlier upped the pressure on the EU by warning they could force a “no deal by accident” scenario.
He said that would open up a “fissure” which would change the British public’s attitudes to the EU for a generation.
Mr Hunt called for “more flexibility and creativity” from Brussels to secure a deal, on his trip to Berlin.
His visit to the German capital marks the start of a cabinet tour of European capitals over the summer, as the clock counts down to Brexit day on 29 March next year.
It comes after Brexit Secretary Dominic Raab did not deny reported Whitehall plans to stockpile foods and medicines and close a major motorway in Kent to turn it into a lorry park, as emergency contingency measures.
The head of Amazon has also predicted “civil unrest” if ministers fail to secure a deal with Brussels, according to The Times.
Doug Gurr, the British manager for the US online giant, reportedly said it was the worst-case outcome.