According to the Europa Press news agency, the magazines were of the type used for assault rifles such as the AK-47, but a police spokeswoman was unable to confirm this when contacted by AFP.
The interior ministry said the two men were Spanish and had been detained for "glorifying terrorism," without giving any further details.
The arrests come as Spain strengthens security during the holiday season.
Authorities in Madrid are taking unprecedented measures for New Year's Eve, when thousands gather in the central Puerta del Sol square for traditional celebrations that see Spaniards swallow 12 grapes for each stroke of midnight.
Bollards will be used on nearby roads alongside police vans to guard against truck attacks like those that hit Nice in France in July, and Berlin on December 19.
Barcelona has taken similar measures.
According to Spanish authorities, 175 alleged jihadists have been detained since 2015, when Spain increased its terror alert to category four on a five-point scale.
Spain has been mentioned on extremist websites as a possible attack target for historical reasons, given much of its territory was under Muslim rule from 711 to 1492.
But unlike France or Belgium, the country is less exposed to the risk of return of radicalised nationals who went to fight abroad and plan to commit extremist acts on home soil.
Madrid, however, was hit by coordinated train bombings by an Al-Qaeda inspired group in March 2004 that left 191 dead.
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