Sources close to the investigation said the theft appeared to have been a highly-professional operation which took place while the owner was away, with the perpetrators disabling the alarm system.
The thieves, who left no trace of their handiwork, had tracked the owner's movements to ensure he did not return to his apartment to catch them red-handed, they said.
El Pais quoted the sources as saying the artwork, comprising portraits and landscapes, was stolen last June. It was not immediately clear why news of the theft was not made public until now.
It was also unclear exactly which paintings were involved but one contemporary art specialist told the paper they would be extremely difficult to sell.
"It is not at all easy to sell a Francis Bacon, large or small without that getting to the ears of those who pore over such a rarified sector," said the expert, speaking on condition of anonymity.
El Pais said police from a specialist arts and antiques unit had opened an investigation into the heist.
The owner of the paintings was a close friend of Bacon, the paper said.
A police spokesman contacted by AFP Sunday was unable to confirm the story.
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Irish-born Bacon died in Madrid in 1992 aged 82 and his expressionist-surrealist works, which are often raw and emotional, remain hugely sought after.
Bacon's death only enhanced his reputation and the 2013 sale of his 1969 work "Three Studies of Lucien Freud" fetched $142,405,000 at auction, a world record at the time.
Art market information leader Artprice lists Bacon as one of 10 frontline modern artists alongside the likes of Picasso and Andy Warhol Warhol whose works comprise 18 percent of global sales