This was the second-highest number in the Championship over that period, with Swansea City recording the most abandoned tests at 15. Portsmouth missed eight.
That means that on a dozen occasions, testers came to North Lincolnshire but players were not available. There is no indication that any Iron players took drugs.
The figure was revealed as part of a Dispatches documentary on Channel Four, which claimed to reveal "the truth" about drugs use in football.
They claimed the 12 abandoned tests at the Iron were among 240 nationwide during the period.
Rio Ferdinand, the Manchester United and England defender, was banned from the game for eight months in January 2004 after missing a test.
Dispatches claimed up to 43 professional footballers have been caught using illegal drugs in out-of-competition testing. These were not performance enhancing.
The program named four of these players, including the Birmingham City forward Gary O'Connor and Rochdale striker Lee Thorpe.
The program alleged cover-ups after players had tested positive for illegal substances at Everton, Nottingham Forest and Tranmere.
There are several instances of players being sacked after testing positive for illegal drugs, with Adrian Mutu and Mark Bosnich having their contract terminated by Chelsea due to their use of cocaine.