Lecuona missed last weekend's European Grand Prix at the same circuit after having to quarantine for 10 days because his brother, with whom he lives in Andorra, had tested positive.
Andorran authorities cleared him to travel to Valencia after he tested negative on Wednesday, but the 20-year-old returned a positive test on Saturday morning.
KTM Tech3 said Lecuona was not showing any symptoms.
Motorcycling
MotoGP star Jason Dupasquier dies after crash
30/05/2021 AT 11:01
"We have sad news today. Although Iker has been tested negative three times, the last test he took this morning at the entrance of the circuit showed positive," team manager Herve Poncharal said in a statement.
"Therefore, he won't be able to enter the circuit and participate at the Gran Premio de la Comunitat Valenciana.
"He will be tested furthermore in order to understand if ever he can fly to Portugal to participate at the last Grand Prix of the season in Portimao."
Lecuona is 17th in the standings with 27 points. He is the second MotoGP rider after Italian Valentino Rossi to miss a race this season due to the novel coronavirus. (Reporting by Shrivathsa Sridhar in Bengaluru; Editing by Kim Coghill)
Motorcycling
Quartararo sets lap record to take pole at Italian GP
29/05/2021 AT 18:04
Motorcycling
IWD special – 'Any sport should be equal' – FHO Racing boss on proving women belong in motorsport
04/03/2021 AT 16:15