Hassan Rowhani, who heads of the Supreme National Security Council, was also quoted by the student news agency ISNA as saying there were "other (nuclear) installations that we have yet to declare and that we only have to declare in due time".
And a statement from the foreign ministry blamed what it said were "misunderstandings" for a report by the International Atomic Energy Agency (IAEA) that criticised Iran for failing to report possible weapons-related activities.
The statement insisted that aside from the criticism, the IAEA's findings highlighted Iran's "total cooperation".
On Tuesday the IAEA issued a report saying Iran had made "omissions" in what was supposed to be a full declaration of its nuclear activities, even though Tehran said it had come clean last October.
A senior Western diplomat in Vienna said the IAEA report showed that Iran's declaration in October "was neither correct nor complete".
According to the report, Iran had withheld its designs for sophisticated "P-2" centrifuges for enriching uranium for both civilian and military uses.
The country also failed to declare that it had produced polonium-210, an element which could be used as a "neutron initiator in some designs of nuclear weapons". Neutron initiators are used to start the chain reaction.
"It was not necessary to inform the IAEA of the research carried out on these centrifuges," countered Rowhani, a cleric charged with negotiations on nuclear issues.
"Iran does not have such centrifuges and is only conducting research and working on a prototype," he was quoted as saying by state news agency IRNA. "We have other research programmes that we do not have to declare to the IAEA."
Rowhani also repeated that Iran's suspension of uranium enrichment -- a key demand of the IAEA -- was "voluntary and this signifies that Iran will one day resume enriching uranium".
The IAEA findings have reinforced the view of the United States that Iran is secretly developing nuclear weapons, an allegation Iran denies.
IAEA director general Mohamed ElBaradei told reporters he hoped "this will be the last time that any aspect of the programme has not been declared to us".
"We have seen some good cooperation from Iran, particularly with regard to access to sites," he said, but added he wanted to see "more prompt, detailed information coming from Iran".
He called the failure to report the P-2, a gas centrifuge design that Iran procured through a global black market from Pakistan, a "setback".
The IAEA report said an Iranian scientist has confirmed experiments with polonium but Tehran has offered an explanation involving the material's civilian uses, such as in power generation.
The report is to be reviewed when the IAEA's 35-nation board of governors meets on March 8 to rule both on Iran's cooperation and Libya's effort to dismantle programmes to develop weapons of mass destruction.
Iran's foreign ministry said any criticisms had merely stemmed from "misunderstandings".
"The rare points on which the IAEA has voiced concern do not cast any doubt over the peaceful nature of Iranian nuclear activities," spokesman Hamid Reza Asefi said in a statement.
"They are misunderstandings that will soon be removed. Otherwise, this report confirms the total cooperation of the Islamic republic."