Gareth Turnbull said his "complete exoneration" from a doping charge raises "serious questions" about the Irish Sport Council (ISC).
Turnbull in action for Ireland in the 2003 World Championships
Turnbull said the verdict had shown the "inescapable conclusion that the terrible accusations made against my name have been ill-founded".
The 27-year-old said the Irish Sports Council had failed to act in the best interests of fairness or justice.
The ISC said Turnbull had been cleared but said the verdict could be appealed.
The middle distance runner said he had never and would "never take or condone in any way the use of prohibited substances in sport".
"Such actions will only ever serve to cheat their competitors, their friends and family and ultimately the athlete themselves.
"Yet my case has unfortunately illustrated how the good name of athletics can be brought into disrepute not by an athlete, but rather from an over-zealous anti-doping programme run by the Irish Sports Council, intent on obtaining an outcome in the best interests not of fairness or justice but of its own sporting and political agenda."
At no time during the past three months have I had less than the 100% support of my peers
Turnbull added that he had been "further saddened by the complete lack of support and sensitivity afforded to me by Athletics Ireland during this entire investigation".
"I can only hope that both organisations will be sincere in their willingness to accept the nature of their failings and learn from them so that any future cases will be treated in a much more professional manner."
Turnbull said Friday's verdict did offer some closure after "what has been a most stressful and difficult four months for not only myself, but my family and friends".
However, he insisted that the decision was "not a final chapter in my case".
"Too many people have worked too hard on my behalf to prove my innocence. This experience has highlighted so many of the reasons why I love my sport.
"I can honestly state that at no time during the past three months have I had less than the 100% support of my peers and those I have encountered within my wider athletic circle, something that I will always have immense gratitude for.
The panel found on the balance of probability, Turnbull had convinced it that the abnormal level of testosterone was not due to doping
Irish Sports Council statement
"My case does raise serious questions about the conduct of the Irish Sports Council and in the coming days we will be pursuing answers and recompense for the damage caused."
The ISC's statement said that the Irish Sport Anti-Doping Disciplinary Panel "had determined that Gareth Turnbull....did not commit an anti-doping violation".
"The Disciplinary Panel found a sample of Mr. Turnbull's urine collected during out-of-competition testing on 30 September, 2005 contained a concentration of testosterone which was not consistent with normal endogenous production.
"Based on the evidence given to it, including the particular unusual scientific facts of this case, the panel found that on the balance of probability, Turnbull had convinced it that the abnormal level of testosterone was not due to doping.
"There is a right for all parties, including WADA and IAAF, to appeal this decision within 14 days of today's date. The matter is therefore sub-judice."
An Athletics Ireland source told the BBC that it was "very happy" with Friday's news but the athletics governing body did not make any official comment on the verdict.