Salvador Illa also said that the second leg of Getafe's Europa League last 32 tie with Inter Milan on March 19 would also be played without fans in the stands.
“The decision of the authorities is that these matches are to be played behind closed doors,” Illa told reporters.
Illa said “a large gathering of fans” needed to be avoided for both matches as Valencia look to overturn a 4-1 first-leg deficit at the Mestalla stadium on March 10.
A Spanish sports journalist who covered the first match at the San Siro on February 19th was diagnosed with coronavirus on his return home to Valencia.
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The Spanish government has made the decision to close the match to supporters due to the “large presence of fans” from area of northern Italy most affected by the coronavirus outbreak, said Illa.
Atalanta are based in Bergamo in Lombardy, the region that has so far been worst hit in Italy by an epidemic that has killed 79 people and infected more than 2,500.
Up to now 150 cases of coronavirus have been detected in Spain according to the latest official figures.
Basketball matches between Spanish teams and clubs in northern Italy have also been affected, with Valencia v Olimpia Milan on March 5 in the men's EuroLeague and Girona v Venezia in the Women's Eurocoupe on March 19th closed off to supporters.