Federica Mogherini's comments, in a joint press conference with Iran's Foreign Minister Mohammad Javad Zarif, underscored tension in Tehran over the accord, which has been in force for three months.
Under the deal, all nuclear-related sanctions were lifted but Iranian officials have accused the West, particularly the United States, of failing to honour its side of the bargain.
Among their grievances is the contention that US government officials are scaring off European banks from investing in Iran for fear of falling foul of regulations that saw massive fines imposed in recent years.
But Zarif echoed remarks from other Iranian officials about the deal not producing discernible benefits.
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"It is necessary that the other side's cooperation, especially the United States, is made good in practice, not only on paper," Zarif said, alluding to Seif's comments.
"We warned the US and we will put some pressure on them, to pave the way for cooperation between non-US banks and the Islamic Republic of Iran."
"We obviously have not finished the work on implementing the JCPOA," Mogherini said, referring to the nuclear deal by its official name, the Joint Comprehensive Plan of Action, describing it as "an ongoing task".
Put to her by a reporter that the banking issues were obstacles, Mogherini countered: "There are challenges in implementation, it is true."
She cited 50 pages of guidelines that have been issued to European financial institutions that detail how business can now be conducted with Iran.
Mogherini pointed to other evidence of cooperation, saying the EU has agreed to support Iran's bid to join the World Trade Organization (WTO) for example, and Iran will take part on a joint dialogue on human rights.
But Mogherini also raised with Zarif the EU's concern about recent ballistic missile tests by the elite Revolutionary Guards, which a UN panel said breached Security Council resolutions.