Aragon claims they were sold illegally by the monastery's nuns.
The seizure comes as tension continues between Madrid and Catalonia over the region's independence push.
Dozens of people protested outside the Lleida museum against the operation, which started at 04:00 (03:00 GMT) and was ordered by Spain's culture ministry.
The legal dispute over the items dates back to the 1980s when the artworks were purchased by the Catalan government. But a court declared the sale null and void in 2015.
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Pro-independence groups have called for more demonstrations in front of the museum. The sacked former Catalan leader, Carles Puigdemont, accused the Spanish authorities of plundering Catalonia.
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