Charles Michel suggested a deal was still possible, but there was no certainty one would be secured in the next two weeks.
The former prime minister of Belgium insisted Brussels was willing to make it happen, but it needed a serious response from the UK Government.
He said: “In my opinion it’s very clear that it is necessary to work seriously, [which is] what we are trying to do, with full trust for Michel Barnier and his team, and we will assess in the next days or in the next weeks, when we consider it is time to assess, what is the result of the talks that are ongoing.
“We all know that in all negotiations, the last and final decisions are the most difficult.
“Will we get a deal? I don’t know. It will depend on what will be on the table.
“But we are working in order to make sure all member states are well informed, are involved in the process in order to make sure there is confidence – which is key in order to able to decide.”
The outstanding issues are on state aid, fishing and governance, with the German EU affairs minister Michael Roth urging the UK to make compromises.
Mr Michel admitted this was a concern, but pointed out they were not new problems.
He explained: “It is not a surprise. You know what are the most difficult topics, and we are working to try to find solutions on the most difficult topics.
“It’s not possible for me to assess what will happen in the next days or in the next two weeks.”
EU officials have suggested mid-November is the absolute deadline for a deal.
Mr Johnson has previously claimed the UK must now prepare for an Australian-style deal on future trade with the European Union, which will see tariffs on exports.
Despite the suggestion this was the end of talks, both sides continued to discuss a deal and nothing has changed.
EU chief negotiator Michel Barnier is expected to stay in London until tomorrow, with talks to end the deadlock on fish taking place today.