BRUSSELS — European Commission President Ursula von der Leyen said "substantial progress" had been made in Brexit talks after a phone call with UK Prime Minister Boris Johnson on Thursday but admitted "big differences remain" and "bridging them will be very challenging".

During the phone call, Johnson "underlined that the negotiations were now in a serious situation" and that "time was short" to reach a deal, according to a Downing Street spokesperson.

With just two weeks to go before a potentially chaotic economic split, hopes had risen over the past few days about the prospects of a breakthrough.

However, everyone concerned knows that there really is very little time left for the remaining differences to be ironed out by Dec. 31 when the transition period formally ends.

The European Parliament even issued a three-day ultimatum earlier to negotiators to strike a trade deal if they are to be in a position to ratify an agreement by the end of the year when the UK leaves the EU's tariff-free single market and customs union.

European lawmakers said they will need to have the terms of any deal in front of them by late Sunday if they are to organize a special gathering before the end of the year.

One of the issues still proving an obstacle to an EU-UK trade deal is fishing rights, according to a statement posted on von der Leyen's Twitter account.

"This evening I took stock with UK Prime Minister Boris Johnson of the on-going negotiations for a comprehensive Partnership Agreement between the European Union and the United Kingdom," it said.

"We welcomed substantial progress on many issues. However, big differences remain to be bridged, in particular on fisheries. Bridging them will be very challenging".

Following the call, the British premier said that a no-deal Brexit was "very likely" unless the EU's position shifted "substantially". He also said that the EU's stance on fisheries was "simply not reasonable".

In a statement released by Downing Street following the call, a spokesperson said: "He (Johnson) said that we were making every effort to accommodate reasonable EU requests on the level playing field, but even though the gap had narrowed some fundamental areas remained difficult.

"On fisheries, he stressed that the UK could not accept a situation where it was the only sovereign country in the world not to be able to control access to its own waters for an extended period and to be faced with fisheries quotas which hugely disadvantaged its own industry.

"The EU's position in this area was simply not reasonable and if there was to be an agreement it needed to shift significantly".

Trade negotiations are set to continue on Friday. — Euronews