Juncker's comments came a day after the EU’s chief Brexit negotiator Michel Barnier said there was a "disturbing deadlock" over the bill, and not enough progress for leaders to agree at a summit next week to open talks on future relations, AFP reported.
"The British are discovering, as we are, day after day new problems. That's why this process will take longer than initially thought," Juncker said.
"Not in an impossible way, I am not in a revenge mood, I am not hitting the British. The Europeans have to be grateful for so many things Britain has brought to Europe, during war, after war, before war, everywhere and every time.
"But now they have to pay."
The former Luxembourg prime minister added that a row over the rights of three million EU citizens living in Britain was "nonsense".
"I don't even understand this problem. Why not say easily, with common sense, which is not a political category as we know, that things will stay as they are?" Juncker said.
The EU says Britain has to make sufficient progress on three divorce issues – the bill, the rights of EU citizens in Britain, and Northern Ireland – before opening the trade negotiations London wants.
EU sources have put the budgetary commitments it says Britain owes at around 100 billion euros ($118 billion), while Britain says the true figure is about one-fifth of that.
EU leaders meeting in Brussels next week are expected to say that there is not likely to be enough progress until the next summit in December, but that the bloc should begin internal preparations for trade talks now.
Leaders of the 27 remaining EU member states will meet for the summit in Brussels on 19-20 October. They will call on Barnier to begin “internal preparatory discussions” on the transition and trade but will refuse to begin talks with the British.