Floodwaters inundated roadways in Riyadh, Mecca and the mountainous south of the mostly desert kingdom, the directorate said in a statement.
Videos posted on social media showed cars submerged in water in the southwestern city of Abha.
Heavy rains have lashed Saudi Arabia for several days and the education ministry closed schools in and around the capital Riyadh on Wednesday.
Red alert weather warning in south Saudi: this video shows Abha in Asir province experiencing severe flooding today. pic.twitter.com/Mv9Ccdd15z
— Rori Donaghy (@roridonaghy) April 14, 2016
Schools shut in Riyadh today, after Saudi hit by rare severe storm leading to flooding last night. pic.twitter.com/aD4zeVRf6B
— Rori Donaghy (@roridonaghy) April 13, 2016