The EU's chief negotiator Michel Barnier lodged his warning at the close of the seventh round of trade talks, which again got stuck on key issues, mainly fishing rights and competition rules, AFP reported.
Hundreds of negotiators met over several days in the Belgian capital with both sides acknowledging a sliver of progress on technical issues – but not on the main obstacles.
"Those who were hoping for negotiations to move swiftly forward this week will have been disappointed," Barnier told reporters after the talks ended in Brussels.
"And, unfortunately, I too am frankly disappointed and concerned and surprised as well," he added.
UK: EU blocking progress
But Britain blamed the European Union for holding up the talks, with a senior British negotiating official pointing to the EU’s insistence that state aid and fisheries policy must be agreed before talks can move on, Reuters reported.
“The process block now is the EU’s insistence that we must accept their position on state aid and fisheries before we can talk about anything else,” the official said.
“We are ready to talk about everything. It’s not us that’s slowing it down.”
Also, Barnier’s UK counterpart David Frost countered that Brussels' insistence that London meet EU demands on state aid and fisheries policy before work on other areas made it "unnecessarily difficult to make progress".
Frost reiterated that he thought a deal remained possible and was Britain's aim but he warned: "It is clear that it will not be easy to achieve," AFP reported.
Barnier said that "too often this week it felt as if we were going backwards rather than forwards."
"At this stage an agreement between the UK and European Union seems unlikely.
"I simply do not understand why we are wasting valuable time," he said.
Britain left the EU in January, nearly four years after a landmark referendum to end almost 50 years of European integration.
Both sides are pushing to have a deal in place by the end of a post-Brexit transition period that ends on December 31.
The Europeans said this requires an agreement by October, leaving just two more months to find common ground.
If no deal is struck, ties will default to minimum standards set by the World Trade Organization, bringing higher tariffs and making onerous demands on business which threaten chaos on the cross-Channel border.
The next round of talks will be held in London on September 7, with an EU summit planned for October 15-16 seen as the unofficial deadline for a deal.
A senior UK negotiating official said Frost would be in "close contact" with Barnier over the next couple of weeks before the next round of talks.