IRNA reported that a Guards helicopter had boarded and taken into Iranian waters the Portuguese flagged MSC Aries.
Shipping security agencies had earlier reported a vessel being boarded and seized by regional authorities in the Hormuz Strait between the United Arab Emirates and Iran.
The Aries is leased by international shipping line MSC from Gortal Shipping, an affiliate of Zodiac Maritime, Zodiac said in a statement, adding that MSC is responsible for all vessel activities. Zodiac is partly owned by Israeli businessman Eyal Ofer.
The incident comes amid rising regional tensions since the start of Israel's campaign in Gaza in October last year, with Israel and its ally the United States clashing repeatedly with Iranian-aligned groups in Lebanon, Syria, Iraq and Yemen.
Iran had threatened to retaliate for suspected Israeli airstrikes on its consulate in Syria's capital Damascus on April 01 that killed seven Revolutionary Guards officers including two senior commanders.
US President Joe Biden said on Friday he expected Iran to attack Israel sooner, rather than later and warned Tehran not to proceed.
Israel's military spokesperson, Rear Admiral Daniel Hagari, said "Iran will bear consequences for choosing to escalate this situation any further", in response to reports of the seizure of MSC Aries.
On Tuesday the naval head of the Revolutionary Guards, Alireza Tangsiri, said it could close the Strait of Hormuz if deemed necessary.
He said Iran viewed as a threat Israel's presence in the UAE, with which Israel established diplomatic relations in 2020 as part of the "Abraham Accords" mediated by the United States.
Yemen's Houthi group has disrupted global trade in the Red Sea for months, saying it is aiming at vessels linked to Israel in retaliation for Israel's campaign in Gaza.
The United States and Britain have carried out strikes against Houthi targets in response to the attacks on shipping.
The Joint Maritime Information Center, run by a Western-led naval coalition, said vessels intending to navigate the Strait of Hormuz, one of the world's most important energy routes, should exercise caution and not loiter.
