"Huijsen, 20, arrived at the national team's training camp on Monday evening but did not train on Tuesday after reporting symptoms of muscle fatigue," the RFEF said in a statement.
"Medical examinations conducted on Wednesday confirmed the muscle injury, of which Real Madrid has been informed, prompting his withdrawal from the squad. We wish him a swift recovery."
Spain are set to face Georgia in Elche on Saturday before hosting Bulgaria in Valladolid on Tuesday as they aim to secure their place in the 2026 World Cup.
The absence of youngster Huijsen, who has impressed at Real Madrid under coach Xabi Alonso following a 50 million pound close-season transfer from Bournemouth, is a setback for Spain manager Luis de la Fuente.
However, Athletic Bilbao defender Laporte, 31, brings vital experience as he was a key player in Spain's European Championship-winning squad last year.
Spain currently top Group E of European qualifying with six points from two matches, with Georgia and Turkey trailing by three points.