"We invite Iran to reverse the steps and go back to full compliance," Federica Mogherini said on Monday.
Iran stepped up production of enriched uranium, used to make reactor fuel but also potentially nuclear bombs, in May.
It is responding to sanctions imposed by the US since it withdrew unilaterally from the agreement.
The breaches come amid heightened tensions between Iran and the US.
There has been tension with the UK, too, following the UK seizure of an Iranian oil tanker earlier this month suspected of taking oil to Syria in breach of sanctions. Iran denies this.
The long-term nuclear deal involves Iran limiting its nuclear activities in return for the easing of economic sanctions, which have badly hurt its economy.
"Technically all the steps that have been taken, and that we regret have been taken, are reversible," Ms Mogherini said, following a meeting of EU foreign ministers.
She said none of the signatories to the deal considered the breaches to be significant, and so they would not be triggering its dispute mechanism which could lead to further sanctions.
The meeting in Brussels was focused on reducing tensions with Iran and ensuring the nuclear deal remains in place.
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