A heavy-water plant and a yellowcake production plant were struck, IRNA reported.
Yellowcake is a concentrated form of uranium after impurities are removed from the raw ore.
Heavy water is used as a moderator in nuclear reactors.
Iran's Atomic Energy Organisation said the Shahid Khondab Heavy Water Complex in Arak and the Ardakan yellowcake production plant in Yazd Province were targeted, the agency said.
The strikes did not cause any casualties and there was no risk of contamination, it said.
Israel also attacked the Arak plant last June.
The International Atomic Energy Agency said there was no increase in off-site radiation levels after the Ardakan site attack.
Word of the attacks came after US President Donald Trump claimed talks on ending the war were going well and gave Iran more time to open the Strait of Hormuz.
Iran's response to a US peace proposal aimed at ending the war was expected later on Friday, according to a source briefed on the matter.
Trump and top White House officials have been told via interlocutors that Iran's counter-proposal would likely arrive on Friday, the source said.
The war, which began when the US and Israel attacked Iran on February 28, has spread across the Middle East.
Iran had been reviewing a 15 point proposal, sent via Pakistan, that included demands ranging from dismantling Iran's nuclear program to curbing its missile development and effectively handing over control of the Strait of Hormuz, according to sources and reports.
An Iranian official told Reuters on Thursday that senior officials had reviewed the proposal and felt it served only US and Israeli interests.
But the official said diplomacy had not ended.
Iran has expressed willingness to talk about certain things in an exchange of messages, US Secretary of State Marco Rubio told reporters after a G7 meeting in France on Friday.
"We're waiting for further clarification about who it is that we would be talking to, what we would be talking about, and when will we be talking," Rubio said.
"It could happen in any moment. It could happen today. Could happen tomorrow."
Air raid sirens sounded in Israel and the military said it has been intercepting Iranian missiles on a daily basis.
Defence Minister Israel Katz said Iran "will pay heavy, increasing prices for this war crime".
"Despite the warnings, the firing continues," Katz said.
"And therefore attacks in Iran will escalate and expand to additional targets and areas that assist the regime in building and operating weapons against Israeli citizens."
Israel's military said its attacks on Friday targeted sites "in the heart of Tehran" where ballistic missiles and other weapons are produced.
It said it also hit missile launchers and storage sites in western Iran.
The United Nations Security Council will engage in a closed consultation on Iran on Friday, according to two UN diplomats.
They said Russia requested the meeting and that the US - which holds the Security Council presidency - scheduled it.
Jan Egeland, secretary general of the Norwegian Refugee Council, said its teams in Iran have reported "countless homes, hospitals and schools have been damaged or destroyed" and that nearly every neighbourhood in Tehran has sustained damage.
"Civilians are paying the highest price for this war - it must end," Egeland said in a statement.
The UN's International Organisation for Migration said on Friday that 82,000 civilian buildings in Iran, including hospitals and the homes of 180,000 people, are damaged.
"If this war continues, we risk a far wider humanitarian disaster," Egeland said.
"Millions could be forced to flee across borders, placing immense pressure on an already overstretched region."
with AP
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