The Gulf sultanate's official news agency initially reported on Sunday that nine schoolchildren and three other adults had "lost their lives after their vehicles got swept away in gushing wadi waters".
Five individuals were also reported missing in the floods that struck the northeast of the country.
The Oman News Agency reported on Monday the bodies of a child and three further individuals and had also been recovered.
Violent thunderstorms, heavy rain and strong winds beginning on Sunday have battered the country, causing flash floods in several regions in the north and east of Oman.
The sultanate's Council of Ministers said in a statement it was "filled with grief" and "extends its sincere condolences and sympathies to the families and relatives of school students who recently died in the Governorate of A'Sharqiyah".
On Monday, the Ministry of Education shuttered schools in most regions as a precaution against the flooding which also resulted in the closure of a number of roads.
Dozens left stranded were rescued in operations aided by helicopters from Oman's air force.
Storms were expected to affect other Gulf states, including Bahrain and the United Arab Emirates, later in the day.
Flooding had already claimed the lives of three children during downpours in Oman in February.
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