The statement by Deputy Foreign Minister Abbas Araghchi suggested tough talks ahead, constituting a rejection of a central demand by the six countries.
At the same time, neither side can afford to have the talks fail.
Lack of agreement would leave Iran struggling under the weight of harsh economic sanctions and a threat of military strikes by Israel, which sees Iran's nuclear program as an unacceptable security threat primarily designed to develop weapons.
The United States has promised to protect Israel, but said more time is needed for diplomacy and sanctions to try to reduce the threat Israel faces from Iran.
The talks are designed to build on a first-step deal that came into effect last month and commits Iran to initial curbs on its nuclear program in return for some easing of sanctions. The deal can be extended, if both sides agree to do so after six months.
Iran insists it is not interested in producing nuclear weapons, but the six powers want Tehran to back its words with concessions.
They seek an agreement that will leave Iran with little capacity to quickly ramp up its nuclear program into weapons-making mode with enriched uranium or plutonium, which can be used for the fissile core of a missile.
For that, they say Iran needs to dismantle or store most of its 20,000 uranium enriching centrifuges, including some of those not yet working. The six powers also demand that an Iranian reactor being built be either scrapped or converted from a heavy-water setup to a light-water facility that makes less plutonium.
Iran is desperate to shed nearly a decade of increasingly strict sanctions on its oil industry and its financial sector in exchange for meeting the six-power demands. But it is fiercely opposed to any major scaling back of its nuclear infrastructure.
"Dismantling (the) nuclear program is not on the agenda," Araghchi told reporters in Vienna.
The talks are formally led by Catherine Ashton, the EU's top foreign policy official, and Iranian Foreign Minister Mohammad Javad Zarif. The United States, Russia, China, Britain, France and Germany are also at the table.
Ashton's spokesman, Michael Mann, warned of the "intensive and difficult work lying ahead of us."
Araghchi said the talks got off to a "very good beginning." But he tempered expectations, saying that even if the negotiations end later this week with nothing more than a future agenda "we've accomplished a lot."
Under the first step deal reached in November and implemented in January, Iran began to carry out a series of steps over six months. They include diluting or converting its stockpile of higher enriched uranium that can be turned quickly into weapons-grade material and not to make any more for the next six months.
Iran also agreed not to increase its stockpile of lower-enriched uranium and not to set up new centrifuges at its enrichment plants as well as to rigorous oversight of the implementation of its commitments by the U.N. nuclear agency.
Sanctions to be suspended in return over the duration of interim agreement include those on Iran's petrochemical exports, its trade in gold and precious metals, its car industry and the supply of parts for Iran's civil aviation industry. There will be no new sanctions as long as the first step deal remains in effect.
For the U.S. administration, successful talks would be a major step toward rapprochement with a country that transformed from a close regional partner to a bitter rival after the 1979 revolution that toppled Shah Mohammad Reza Pahlavi and installed the Islamic Republic under the late Ayatollah Ruhollah Khomeini.
Critics in the U.S. and Israel will be closely watching the negotiations, fearful that the White House might concede too much in hope of striking a historic bargain. Hardliners in Iran are also wary of any deal they see as rolling back Iran's hard-won nuclear accomplishments.
Margaret Childs in Vienna contributed to this report.
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