EastEnders won the 'Soap and Continuing Drama' award at the ceremony last Sunday (May 12).
However, Coronation Street won 'Best Soap' at the British Soap Awards on Saturday (May 18) as well as scooping seven other awards. EastEnders went home with one.
Speaking to The Mirror, Blackburn said: "EastEnders has not had a brilliant year and Corrie's at its best. But them's the breaks.
"There were six, seven people on that panel, they made a decision. They were clearly wrong."
A Coronation Street insider also added that the ITV show actors felt "vindicated".
The source said: "How EastEnders won the BAFTA is a mystery to the Corrie cast. As far as they're concerned, it's normal service resumed. Corrie continues to go from strength to strength."
EastEnders' only victory at the Soap Awards was a Lifetime Achievement accolade for Adam Woodyatt, who plays Ian Beale.
Coronation Street's success included 'Best Soap', 'Best Actor', 'Best Storyline', 'Best Villain', 'Best Exit', 'Best Dramatic Performance' and 'Sexiest Female'.
The British Soap Awards 2013: Winners
Digital Spy Soap Scoop video - press play below to watch Amie Parker-Williams reveal gossip on Tina's labour scenes in Coronation Street, a baby bombshell in Emmerdale, danger for Dodger in Hollyoaks and a possible romantic reunion in EastEnders.