"We are in the middle of talks about nuclear proliferation and reining in Iran's programme, it is a really tough negotiation I will tell you," Kerry said in the Austrian capital.
He said later after the talks with Iranian Foreign Minister Mohammad Javad Zarif: "We are working, we are working very hard. Serious discussions. (It was a) good meeting."
A senior US official said there was "more work to do".
The deadline for Iran and the five permanent members of the UN Security Council plus Germany to get a deal is Sunday, when an interim accord from November expires.
This can be extended, allowing both sides to continue talking, but only if both sides agree and Washington insists Iran has to make major concessions first.
Kerry was due to give a news conference on Tuesday morning, the US official said, and it was unclear whether he would hold any more discussions with Zarif.
Egyptian state media reported that Kerry was due in the country in an effort to broker a truce in Gaza.
The Iran talks, which entered their sixth and final round on July 3, were however set to continue between lower-ranking officials and may go down to the wire of the July 20 cut-off point.
The mooted accord would kill off for good fears that Iran might develop nuclear weapons under the guise of its civilian programme after a decade of rising tensions and threats of war.
Iran denies seeking the atomic bomb and wants the lifting of crippling UN and Western sanctions.
The six powers want Iran to dramatically reduce in scope its nuclear programme - for at least 10 years, Washington says - and agree to more intrusive UN inspections.
This would greatly expand the time needed for the Islamic republic to develop a nuclear weapon, should it choose to do so, while giving the world ample warning of any such "breakout" push.
But Iran on the other hand wants to expand its nuclear facilities, insisting they are purely peaceful and that it has the perfect right to do so.
Both sides are also under intense domestic pressure from hardliners both in Iran and in Washington - midterm US elections are in November - both wary of giving too much away.
Kerry, along with the foreign ministers of France, Germany and Britain and the deputy foreign minister of China jetted into the Austrian capital on Sunday seeking to inject some momentum.
But the three European ministers left on Sunday evening empty-handed, leaving Kerry, fresh from successfully defusing Afghanistan's political crisis, to keep trying.
Britain's Foreign Secretary William Hague said there had been no "decisive breakthrough" on Sunday and a "huge gap" remained on the key issue of uranium enrichment.
This activity can produce fuel for the country's sole nuclear plant or, if further enriched, the material for an atomic bomb.
Israel, the Middle East's sole if undeclared nuclear armed state and which together with Washington has refused to rule out military action, is opposed to any enrichment by Iran at all.
Israeli Prime Minister Benjamin Netanyahu warned on Fox News Sunday that any deal leaving Iran with the capability to pursue this activity would be "catastrophic".
Iranian negotiator Abbas Araqchi was Sunday publicly sticking by Iran's position on enrichment which he called "clear and rational".
"As the supreme leader said, the enrichment programme has been planned with the real needs of the country in mind, meaning our need to ensure reactor fuel."
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