Major differences remained and they were "well away from an agreement", IMF spokesman Gerry Rice told reporters.
Greece is seeking a cash-for-reform deal, to avoid defaulting on a €1.5bn debt repayment to the IMF.
But the European Council president said there was no more time for gambling and the game would soon be over.
"The Greek government has to be, I think, a little bit more realistic,'' Donald Tusk said.
Greek Prime Minister Alexis Tsipras held talks with European Commission head Jean-Claude Juncker in Brussels on Thursday afternoon but little progress was made.
He also held a late-night meeting with the French and German leaders on Wednesday, after which Mr Tsipras said they had decided to intensify talks.
The EU and IMF are unhappy with the extent of economic reforms the Athens government is offering in exchange for the release of a final €7.2bn (£5.3bn) in bailout funds. Their bailout deal with Greece runs out at the end of June.
Mr Tsipras's left-wing Syriza party came to power in January on an anti-austerity platform.
IMF's Gerry Rice in Washington said there had been "no progress" in narrowing differences during the talks between IMF and Greek negotiators in Brussels, and both teams had packed up and left for home.
But he stressed that "the IMF never leaves the table. We remain engaged - but the ball very much is in Greece's court right now."
He said the sticking points remain pensions, taxes and financing.
Analysis: BBC's Chris Morris in Brussels
Sometimes the toughest talking happens just before a deal is done.
But occasionally it means things are about to fall apart.
So the public pressure on Alexis Tsipras is growing - reflecting concern within the EU and the IMF that he has miscalculated the extent to which he can orchestrate a change in policy.
But there are countervailing pressures on the prime minister at home. His supporters swept his party to power in January and now they expect him to deliver - and some are taking a hard line.
Tsipras's impossible position
Greek spokesman Gabriel Sakellaridis said in a statement that government negotiators were ready to intensify talks "even in the coming days" and would carry on working on the remaining issues "such as the fiscal issue and the sustainability of the debt".
Earlier in the day, Greek stocks had soared by more than 8% after EU Commissioner Pierre Moscovici said a debt deal was close and needed a "happy ending".
However, as the mood darkened, stock markets elsewhere began to retreat. By then, the Athens market was already closed.
One EU diplomat called the meeting between Mr Tsipras and Mr Juncker a "last attempt" to reach a debt deal.
"If the process was working properly the president would not have had to have a meeting with Tsipras today," he was quoted as saying.
Mr Tsipras told reporters after meeting Mr Juncker that they were "working in order to bridge the remaining differences" and reach an agreement "which will ensure that Greece will recover with social cohesion and viable public debts".
The Greek government needs an urgent deal as it is running out of cash and needs the last slice of its bailout money.
One possible solution would be a temporary deal with EU creditors until March, when the IMF part of the bailout also runs out. But if that does not work out, Greece could default and there is a risk it could fall out of the euro.
Is Greece close to Grexit?
Earlier this week, Athens submitted a revised reform plan to the EU and IMF, after Mr Tsipras rejected a set of reforms put forward by Jean-Claude Juncker.
It is believed Athens has conceded some ground on VAT reforms, pensions and the country's primary surplus target.
A major sticking point in the talks appears to be Mr Tsipras's demand for some debt relief for Greece, the BBC's Damian Grammaticas in Brussels reports.
European leaders will not countenance writing off debts before Greece commits to reforms, our correspondent says.
Last week, Greece postponed until the end of June a €300m payment to the IMF, deciding to bundle up four payments amounting to €1.5bn.
Mr Tsipras has warned that a failure to reach a deal on Greece's bailout by the end of June would be the beginning of the end for the eurozone.
Greek state broadcaster goes back on air
Mr Tsipras's left-wing Syriza party fulfilled one of its campaign pledges on Thursday when state broadcaster ERT resumed broadcasts, exactly two years after it was replaced by a smaller-scale operation called Nerit.
Nerit's channels were replaced on Thursday by ERT's programming.
Greece's international creditors have raised the pressure on the Athens government, as IMF negotiators left talks in Brussels and flew home.