The town, in an oil-producing province and home to a large Shia population, is a flashpoint between the Sunni Muslim government and Shias complaining of discrimination.
The soldier was killed by a rocket-propelled grenade in a district of al-Awamiya and operations to counter the militants continued with the help of back-up forces, the ministry said.
Gunmen kill Saudi child, Pakistani in Shia district: ministry
On May 12, authorities said gunmen killed a Saudi child and a Pakistani man during an attack on workers at a building project in al-Awamiya.
In Tuesday's statement, the Ministry said "terrorist elements" were using explosive devices and landmines to obstruct the building project.
Qatif has seen protests for more rights for Shi'ite and these have become more frequent since Nimr al-Nimr, a Shi'ite cleric convicted of inciting violence, was executed a year ago.
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