The club were highlighted in Channel Four's Dispatches documentary on Monday night as having missed 12 unannounced tests in a three year period up to August 2010. This was the second highest in the Championship over the period, second only to Swansea City.
David Beeby, the Iron's general manager, revealed the dates of the abandoned tests.
"One of the visits occured in April 2007 in the week following the team clinching the League One title at Tranmere, when training times changed," he told the club's official website.
"One in April 2008 on the Monday following the 1-0 victory at Watford when the players were given an unscheduled rest fay, and one in July 2010 when the training times changed due to a pre-season friendly at York City."
The club has to provide the Football Association with details of training schedules, giving at least an hour a day when inspectors can turn up unannounced and cary out tests.
"These instances of abandoned tests are innocent mistakes due to changes in our training schedule. Every drug test that has been carried out has had a negative result," added Beeby.
The Football Association have defended their drugs testing procedure after claims more than 40 professional footballers have tested positive for illegal substances.
They defended their policy of not naming players who tested positive for drugs that are illegal but not performance-enhancing .
“Football is one of the only sports in the UK that ban social drugs at all times, and were the first to do so," they said in a statement.
“Any player who tests positive for a social drug out of competition is charged and subject to a sanction which ordinarily includes a suspension from all football activity for a period of up to six months for a first time offence. They are also subject to target testing for a period of two years. The FA do not report the name of the player as this offence is not a WADA Code offence and privacy allows for the player to undergo any necessary rehabilitation and counselling."