The two agencies were 20,800 officers short as of October 31, with only 142,691 in active service instead of the required 163,491, El Pais newspaper reported on Tuesday, citing the ministry's figures.
According to the newspaper, the police had most difficulty filling the vacancies in the provinces of Girona and Leida in Catalonia. The province of Gipuzkoa in the Basque Country is another region with few Civil Guard officers present.
Both regions have a long history of pro-independence movements and both have their own police forces, which are not included in the ministry's data.
In October last year, the Catalan government organized an independence referendum opposed by the central authorities. Madrid engaged police forces to ensure that the vote would not go through, and the actions of police, attempting to stop the voters, were widely debated after the referendum.