Most of these were French and stayed overnight in Spain.
Bars in Madrid remain open until 11pm despite the high number of cases in the region.
Parties have had to be broken up while the municipal police intervened in over 3,700 tourist accommodation sites, such as Airbnb, which did not comply with restrictions.
The problem has arisen because autonomous communities do not have the power to decide on the closure of borders to other countries.
This differs from the central government which has limited travel from the United Kingdom and non-EU countries.
Prime Minister Pedro Sánchez justified the decision not to act on the rest of the EU, stating: “Spain is following the European Union’s recommendations, which recommends keeping the borders open for community travel.
However, the European Commission has intervened on the issue by recommending “consistency” on internal and external travel.
While the French favour the mainland, Germans have been flocking to the Balearic islands.
Bookings from German tourists have boomed after Spanish hotspots such as Palma de Mallorca and Benidorm were axed from the list of areas considered at risk on March 14.
TUI plans to offer more than 300 flights in the coming weeks and Ryanair has already added 200.
According to German news source DW, over 40 thousand Germans will spend the Easter holidays in the Spanish islands.
Under current rules, Britons will be allowed to travel to Spain from March 30 providing they can prove their journey is essential.