Ayatollah Khamenei, who will have the last word for Iran in its talks with the West, made the comments after Iran's parliament passed a bill on the country's nuclear program.
With obstacles remaining just one week until the June 30 deadline for a nuclear deal, the Leader said Iran seeks to reach a fair deal that will serve the country’s national interests.
"All Iranian authorities, while insisting on the red lines, are pursuing a good deal which is a fair and honorable agreement in line with Iran’s interests,” the Leader said in a meeting with the heads of the three branches of power and senior officials here.
Banking and economic sanctions imposed on Iran by the United Nations or U.S. Congress must be lifted immediately when an agreement is signed, Ayatollah Khamenei said.
"Other sanctions can be removed gradually by a reasonable timetable," the Leader added, noting cancellation should not be linked to implementation by Iran of its commitments.
Describing the International Atomic Energy Agency (IAEA) as "neither independent nor fair", Ayatollah Khamenei said Iran would not permit inspections at military sites or "unconventional inspections" at other facilities.
The Leader also called into question the duration of limits under a final accord. A preliminary framework agreed on April 2 stated that Iran's enrichment of uranium would be curtailed for 10 years, with other parts of its nuclear activities being curbed for longer.
Noting that some restrictions are acceptable, "extreme demands" are not, Ayatollah Khamenei said.
"Unlike the insistence from the Americans, we do not accept long-term limitations of 10, 12 years. We have told the negotiating team how many specific years of restrictions are acceptable," Ayatollah Khamenei said. "Research and development must continue during the years of restrictions," the Leader added.
The Leader said the U.S. is offering a "complicated formula" for lifting sanctions. Ayatollah Khamenei added waiting for the UN's International Atomic Energy Agency to verify its cooperation would take too long.
"Lifting sanctions can't depend on implementation of Iran's obligations," the Leader said.
Ayatollah Khamenei said U.S.'s "goal is to uproot and destroy the country's nuclear industry". "They want to keep up the pressure and are not after a complete lifting of sanctions."
Ayatollah Khamenei stated that the Americans are also making efforts to deprive the Iranian nation of the great advantages of the nuclear industry while maintaining pressure and sanctions against the Islamic Republic.
The Leader said Iran has always made rational demands since the beginning of the talks with the P5+1 countries and emphasized that all "cruel sanctions” on Tehran over its nuclear program must be lifted.
Ayatollah Khamenei commended the Iranian nuclear negotiating team for its faithfulness and bravery in the talks with the six world powers, and said the negotiators are meticulously making efforts in order to settle issues.
The Iranian negotiators have managed to bravely announce Iran’s stance on the nuclear issue, the Leader said, adding that they may possibly make some mistakes but they are "brave and faithful”.
He pointed to all nuclear powers’ refusal to sell 20% enriched fuel to Iran for the production of nuclear medicine at the Tehran Research Reactor and said young Iranian scientists have succeeded in producing the fuel and confounding the opposite side.
On Wednesday, the Guardian Council has approved a bill that stipulates all sanctions imposed on Tehran over its nuclear program must be lifted as soon as a nuclear deal with the P5+1 comes into effect.
The council’s spokesman Nejatollah Ebrahimian said the bill was "extraordinarily” discussed and gained the required approval from the supervisory body.
The bill stipulating that all sanctions be lifted as soon as a nuclear accord takes effect was approved by 214 of 244 lawmakers on Tuesday.
State TV said the bill allowed the International Atomic Energy Agency solely to inspect Iran's nuclear installations under its existing Safeguards Agreement with the IAEA.
"But it bans any inspection of military, security and non-nuclear sites as well as access to documents and scientists."
The bill also obliges Foreign Minister Muhammad Javad Zarif, Iran's top negotiator, to report to parliament every six months on the process of implementing the accord.
"The government must preserve Iran's nuclear rights and achievements ... Any deal reached by the government with the powers must be approved by parliament," national TV said.
Zarif said on Monday he saw a good chance of reaching a final agreement by June 30 or a few days later, provided there was political will to do so.