The warning came in a social media post on X. It included a satellite image of the plant in a red circle like other warnings that proceeded strikes.
The Arak heavy water reactor is 250 kilometres southwest of Tehran.
Heavy water helps cool nuclear reactors, but it produces plutonium as a byproduct that can potentially be used in nuclear weapons.
Iran had agreed under its 2015 nuclear deal with world powers to redesign the facility to relieve proliferation concerns.
The International Atomic Energy Agency has been urging Israel not to strike Iranian nuclear sites.
Already, Israel's airstrike campaign has targeted Iran's enrichment site at Natanz, centrifuge workshops around Tehran and a nuclear site in Isfahan.
US President Donald Trump has told reporters he will not say whether he has decided to order a US strike on Iran, a move that Iranian officials warned anew would be greeted with stiff retaliation if it happens.
"I may do it. I may not do it. I mean, nobody knows what I'm going to do," he said, outside the White House.
Trump said Iranian officials had reached out about negotiations including a possible meeting at the White House but "it's very late to be talking," he said.
"Unconditional surrender, that means I've had it."
Asked for his response to Iranian Supreme Leader Ayatollah Ali Khamenei rejecting the idea of surrendering, Trump said: "I say, good luck."
People jammed highways out of the capital Tehran, a city of 10 million people, as residents sought sanctuary from intensified Israeli air strikes.
In its latest bombing run, Israel said its air force destroyed Iran's police headquarters.
"As we promised - we will continue to strike at symbols of governance and hit the ayatollah regime wherever it may be," Defence Minister Israel Katz said.
Israeli strikes on Iran have killed at least 639 people and wounded 1,329 others, according to Washington-based group Human Rights Activists.
Khamenei, 86, rebuked Trump in a recorded speech played on television, his first appearance since Friday.
The United States "should know that any US military intervention will undoubtedly be accompanied by irreparable damage," he said.
"Intelligent people who know Iran, the Iranian nation and its history will never speak to this nation in threatening language because the Iranian nation will not surrender."
Trump has veered from proposing a swift diplomatic end to the five-day-old war to suggesting the United States might join it.
A source familiar with internal discussions said Trump and his team were considering options that included joining Israel in strikes against Iranian nuclear installations.
Defense Secretary Pete Hegseth told a Senate committee that the Pentagon was prepared to execute any order given by Trump.
Israel's military said 50 Israeli jets struck about 20 targets in Tehran overnight, including sites producing raw materials, components and manufacturing systems for missiles.
It advised Iranians to leave parts of Tehran for their own safety while it bombed targets.
Arezou, a 31-year-old Tehran resident, told Reuters by phone that she had made it out to the nearby resort town of Lavasan.
" My friend's house in Tehran was attacked and her brother was injured. They are civilians," she said.
"Why are we paying the price for the regime's decision to pursue a nuclear program?"
In Israel, sirens rang out warning people of retaliatory Iranian missile strikes.
with AP
