Popov had agreed terms to join Rovers after completing a medical last week but the Home Office refused him a permit because he had not played in enough internationals, the Bulgarian champions said on Wednesday.
The 22-year-old, who has scored three goals in 15 matches for Bulgaria, made his debut for the Balkan country in a friendly against Wales in 2007 but missed several games in the last year due to injury.
Popov, scorer of 32 goals in 101 matches in the Bulgarian top flight, was instrumental in helping the Lovech club win last season's league title, two national cups and the domestic Supercup.
Bulgarian media reported that Blackburn were ready to pay a transfer fee of three million euros for Popov, who is expected to start for Bulgaria in their Euro 2012 qualifier against England on Friday.
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