"We are concerned by (Akbar Hashemi) Rafsanjani's defeat," the Italian commissioner Franco Frattini told La Reppublica newspaper, referring to the defeated candidate in Iran's vote.
Frattini voiced concern over the stance taken by the Islamic republic's hardline new leader Ahmadinejad over Iran's pursuit of nuclear technology.
"Ahmadinejad has made some very tough inital statements. He says Iran has the right to nuclear development, but we will have to check whether this means for civilian or military uses."
Britain, France and Germany are engaged in talks with Iran in a bid to convince the clerical regime to abandon sensitive uranium enrichment activities, which Iran insists are needed to make reactor fuel but could be diverted to military purposes.
Frattini also argued that Europe could help bridge the gap between Iran and the United States, which suspects Tehran of covertly developing nuclear weapons.
On human rights, he insisted on the need for Tehran to stick to a planned calendar of talks with EU officials on human rights, with the next round set for September, at risk of jeopardising the nuclear negotiations.
"We must stand by our demand that Iran respect fundamental human rights, as we did with outgoing President (Mohammad) Khatami."
Human rights, and women's rights in particular, were "a principle impossible to renounce", Frattini stressed, drawing attention in particular to the issue of stoning.
Executions by stoning have been suspended in Iran since late 2002, when the EU opened long-term trade talks with Iran and made human rights issues a key condition to negotiations.
Human rights activists and diplomats have said Iran appears to have respected the moratorium on stoning although there have been cases of minors being executed.