Emergency teams responded to the incident late on Tuesday and took the necessary measures, the ministry said. No casualties were reported.
Earlier, a company source said a ballistic missile had struck the Aramco headquarters complex, damaging the top three floors of an office tower and causing a fire.
The complex houses a major operations centre for Aramco, which oversees an extensive network of oil rigs, pipelines, refineries and export terminals.
The Houthis have launched ballistic missiles and drones at key Saudi sites over the past week in retaliation for Riyadh’s support for government forces in Yemen’s renewed civil war.
Riyadh’s international airport has been struck four times, including in a Saturday attack that killed 13 people and disrupted air travel across the kingdom.
The Saudi-led coalition said fragments from a missile intercepted over Dhahran fell in a residential area. Authorities also reported intercepting missiles and drones over Riyadh and southern Saudi Arabia.
Saudi Civil Defence said on Wednesday that four people, including two women, a man and a child, were injured after debris from two intercepted Houthi missiles fell in Riyadh. The debris caused limited damage to 15 homes, according to the authority.
The Houthis had threatened a “harsh and painful” response to Saudi-led strikes on Yemen’s capital, Sanaa. Group spokesperson Yahya Saree said potential targets could include the Aramco headquarters in Dhahran and an oil refinery in Riyadh.
The group also warned oil workers in Saudi Arabia to stay away from sites that could be targeted.
The renewed exchanges have also extended to Yemen. Houthi-run Al-Masirah television reported that the Saudi-led coalition had attacked a fuel depot operated by the Yemen Petroleum Company on the outskirts of Sanaa.
The coalition confirmed striking the depot and other locations on Tuesday evening, saying the operation aimed to neutralise the Houthis’ ability to threaten Saudi Arabia, Yemen and international waterways.
Before the attack on Aramco, the Saudi cabinet, chaired by Crown Prince Mohammed bin Salman, had warned that the Houthis would face consequences for their repeated attacks on the kingdom.
The renewed conflict comes as Saudi Arabia seeks to reverse recent Houthi advances along Yemen’s Red Sea coast towards the strategic Bab el-Mandeb Strait.
The waterway, which connects the Red Sea to the Gulf of Aden, has become increasingly important for Saudi and global energy supplies since the wider Iran war began in February and disrupted shipping through the Strait of Hormuz.
A Yemeni government offensive launched a week ago pushed Houthi forces away from areas closest to Bab el-Mandeb. However, the group remains entrenched nearby and has made gains around the city of Taiz this month.
Saudi Arabia has sought greater support from its allies to counter Houthi missile and drone attacks. The United States, Riyadh’s longstanding security partner, has so far resisted Saudi efforts to draw it directly into the conflict against the group.
The renewed fighting is unfolding amid the wider US-Iran war, which began with American and Israeli attacks on Iran on February 28.
Iranian Foreign Minister Abbas Araghchi said on Sunday that Tehran was willing to mediate between Saudi Arabia and the Houthis. The offer was reiterated in statements issued by Iran’s foreign ministry on Monday.
