Sir Ivan Rogers privately briefed government officials that European diplomats believed a deal would not be completed until the middle of the next decade, according to the BBC.
At a meeting of the European Council summit Prime Minister Theresa May said the UK would be looking for a "smooth and orderly" process, and did not comment on time scales. May will not be attending a dinner tonight between European leaders to discuss Brexit.
The issue is highly sensitive for the government, at a time when senior figures – including the chancellor – are publicly pushing for a transitional arrangement.
International trade analysts were split as to the credibility of a 10-year trade deal.
Miriam Gonzalez, a partner at law firm Dechert focused on international trade, said: "What is certainly the case is that this is likely to be more than a two-year process."
A transitional deal is "certainly important for businesses" if that is the case, she added.
"Two years is not a particularly long time to unravel 40 years of legal entanglement," said spokesman for the Institute of Directors. "That isn’t the end of the world as long as there are transitional arrangements."
Quentin Peel, associate fellow with the Europe Programme at Chatham House, said that Rogers’s estimate "sounds realistic erring on the conservative side."
"It’s the most complicated negotiation in living memory," he added, with 27 individual states involved – possibly with different agendas – compared to six when the UK entered the EU.
Squaring European agendas with UK interests will be key to quick negotiations, according to Shanker Singham, director of economic policy at the Legatum Institute.
"Agreements can be done very quickly if countries have ‘offensive’ interests," he said – in other words, if they need access to another country’s businesses or consumers.
Either way, the UK will almost certainly leave the EU. Richard Tice, co-chair of Brexit campaign group Leave Means Leave said: "Mr Rogers, like any similar civil servant, is paid to paint the extremes of possibilities.
"The key point, however, is that we are leaving two years after serving Article 50, with or without a trade deal.
"We can very happily revert to WTO rules which is what the vast majority of countries do with the EU."