Rights campaigners say the weapons contravene a United Nations treaty because they might be used against civilians in Yemen, where a Saudi-led military coalition is battling the Iran-backed Houthis in a war that has killed thousands.
The kingdom mobilised a coalition of mostly Sunni-ruled countries in 2015 to topple the Houthis after they ousted the country's internationally-recognised government.
In a tweet, Saudi Arabia's embassy in Washington said the two missiles had been intercepted in Makkah province, which includes Jeddah and Taif.
The developments come at a time of heightened tensions between Iran and Gulf Arab states allied to the US.
Two pumping stations along Aramco's East-West oil pipeline in Saudi Arabia were attacked by explosive-laden drones last week, the official Saudi Press Agency (SPA) reported, citing Saudi Energy Minister Khalid al-Falih, who described the attack as one of "terrorism and sabotage".
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Saudi Arabia said on Monday that it had intercepted two missiles in Makkah province fired by Yemen's Houthis.
According to Reuters, dockworkers attempted to have the Saudi ship-officially called the the Bahri Yanbu-barred from entering the Port of Genoa. There were no immediate reports of injuries or damage.
The attack bears extra significance at this stage of the war because it indicates that Yemeni forces were able to fly their armed drones a long distance and carry out precision strikes and then fly them back while evading Saudi defenses all along.
The Houthis denied any such missile fire, adding that they would have claimed responsibility if they had been behind a launch.
Saudi Arabia will hold an emergency Arab summit in Mecca on May 30 to discuss the implications of the attacks, which came as the United States and Iran spar over U.S. sanctions reimposed on Tehran and over the USA military presence in the Gulf.