"In light of the severe violation of the cease-fire carried out by the Iranian regime, we will respond with force," Chief of General Staff of the Israel Defense Forces Maj. Gen. Eyal Zamir said in a statement.
The order from Zamir follows Defense Minister Israel Katz saying in a statement reported by local media that he had instructed the IDF to "respond forcefully to Iran's violation of the cease-fire."
The IDF said it had detected two ballistic missiles fired at Israel from Iran.
On X, it earlier said alerts had been activated in northern Israel following the detection of the launches.
Iran has yet to comment.
The implications of the Israeli order and the iran launches were not yet clear, but several Israeli politicians appeared to be calling for renewed attacks on Iran.
"Tehran will tremble," far-right Finance Minister Bezalel Smotrich said on X.
Chairman of the conservative opposition party Yisrael Beiteinu Avigdor Lieberman demanded Israel respond to the alleged cease-fire violation.
"We must not absorb, we must not ignore, we must respond immediately," he said.
The cease-fire between the two countries had gone into effect early Tuesday after the two sides exchanged final volleys of attacks.
The IDF said it had attacked missile launchers in northern Iran shortly before the cease-fire was to take effect, while announcing that there had been several missile launches from Iran toward Israel early Tuesday. Israel said on its X account that at least four people were killed and 22 injured in the attack on Be'er Sheva.
Prime Minister Benjamin Netanyahu announced that Israel had accepted U.S. President Donald Trump's cease-fire proposal in a statement early Tuesday, saying they had achieved their goal in going to war with Iran on June 13.
"In light of the operation's objectives having been achieved, and in full coordination with President Trump, Israel has agreed to the President's proposal for a mutual cease-fire," Netanyahu said, while retaining the right to respond "forcefully" to any Iranian violations of the agreement.
"This is a tremendous success for the people of Israel and its fighters, who have removed two existential threats to our nation and secured the eternity of Israel."
Iranian state-run Press TV announced on X that, as the cease-fire was to begin, Iran was taking "parting shots" at Israel.
Seyed Abbas Araghchi, the foreign minister of Iran, had earlier said their armed forces would continue fighting until the last minute and that they would only silence their weapons if Israel, which he blamed for starting the war, did as well.
Trump announced that the cease-fire had gone into effect early Tuesday on his Truth Social platform, urging both sides not to violate it.
Israel and Iran have been in a proxy war for years, which exploded into the open on Oct. 7, 2023, when Tehran's proxy militia Hamas in Gaza attacked Israel.
Israel responded by devastating the Palestinian enclave, but other Iranian proxy groups, the Houthis in Yemen and Hezbollah in Lebanon, also became involved in the fighting, prompting Israel to attack those militias in the nearby Middle Eastern countries.
Fears that the war would expand throughout the region were inflamed earlier this month when Israel conducted a surprise attack on Iran's nuclear facilities, as well as targeting its air defense systems and killing several of its military leaders.
The United States, under the direction of Trump, then attacked three of Iran's nuclear facilities on Saturday night, which Iran responded to by attacking a U.S. base in Qatar on Monday. No Americans or Qataris were reportedly injured.
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