Addressing a press conference on Wednesday, Ignacio Aguado, the deputy leader of the region with more than 6 million inhabitants, said health authorities would use its remaining BioNtech-Pfizer doses to give the administer the second jab to people who had already received the first one, reports Xinhua news agency.
"Unfortunately, as we suspected, the pace of deliveries was interrupted," he said, adding that the region would "not leave people without the very necessary second dose" of the vaccine.
"If we don't do that (administer the second dose), there is the chance that the virus could mutate and become resistant, and that would lengthen the fight against the pandemic," added Aguado.
Last week, Enrique Ruiz Escudero, who is responsible for the Madrid region's health authority, confirmed that it had suspended its vaccination plan for frontline health workers.
The Spanish Ministry of Health on Wednesday reported that 1,356,461 doses have been administered.
The government had said it hopes to inoculate 2.9 million people by the end of March and around 20 million people by June.
One of the hardest-hit countries in Europe, Spain has so far registered 2,670,102 confirmed coronavirus cases and 57,291 deaths.