The 54-year-old says the demands of the Allsvenskan are to blame for some players feeling the effects of a long season in his Blagult selection ahead of the European Championship
The national-team boss questioned the motives of the domestic governing body, as most of the players involved in the European Championship qualifier were injured going into the match.
Anders Svensson and Tobias Hysen, who form part of Sweden's 23-man squad for Euro 2012, are also suffering from physical and mental fatigue, and Hamren is now looking for answers from the SvFF.
"Swedish football should stop and think if what they are doing is the right thing," he told reporters at a press conference.
"And if this is the way you want to run things, then you are giving your players very little chance to win. This, for me as national-team coach, is unacceptable."
Hamren then suggested that the season in Sweden should have started earlier, while the first rounds of the campaign should be played on artificial grass if weather conditions are poor.
Sweden's top-flight runs concurrently to most other European league, beginning on March 31 and running until November 4, with a break for the European Championship midway through.