According to Channel 12, the container ship, which was reportedly traveling from Tanzania to India, was struck by a small projectile and sustained minor damage. The ship was named the LORI, which is registered in Liberia and owned by Israeli businessman Udi Angel.
According to the paper, Israeli security sources believe the launch was a planned Iranian attack.
The incident was confirmed to Israel's security forces as well as the owners of XT Management, a Haifa-based ship firm.
The ship will proceed to India, where it will be inspected for damage.
Officials claim the attack was in retaliation for an Israeli attack on an Iranian-owned ship off the Syrian coast, which Tehran blamed on Israel.
Another Israeli-owned cargo ship sank in the same area last month after a mysterious blast.
Prime Minister Benjamin Netanyahu blamed Iran for an accident on board an Israeli-owned ship in the Gulf of Oman at about the same time.
A blast above the water line struck the vehicle-carrier MV Helios Ray between the night of Feb. 25 and the morning of Feb. 26, ripping holes in both sides of its hull, according to a US official. According to an Israeli official, limpet mines were used.
At the time, Iran denied any involvement.
"We categorically deny this charge," said Saeed Khatibzadeh, a spokesman for the Iranian Foreign Ministry.