The minister's statement was part of an interview with the Politikaplus portal posted on the operation's recent 17th anniversary.
The three associations find the statement unacceptable, saying it overshadows the steps forward made in building trust in Croatia and better relations with neighbouring countries, and that it brings into question the prerequisites built for unbiased and effective prosecution of war crimes.
The letter says that regardless of when the statement was made, it is harmful for a government about to join the European Union because one of its ministers is bringing into question the rule of law, judicial independence and respect for human rights.
The associations expect the minister to distance himself from those statements and all government representatives to refrain from making statements that bring into question verdicts, judicial work and the rule of law.
They say the government is bringing into question its credibility by paying for the defence of Tomislav Mercep and other war crimes indictees, and by extending the contract with the law firm hired in the appeals proceedings of generals Ante Gotovina and Mladen Markac at the Hague war crimes tribunal.
The associations say it is especially inappropriate for the government to pay for the defence of war crimes indictees "when the Croatian judiciary hasn't convicted even one perpetrator of war crimes committed during or after Storm or paid damages to even one family of Serb civilians killed in the operation."
The associations say it would be much more just and dignified if the government directed those budgetary funds into paying damages to war crimes victims.
They say the statements made by President Ivo Josipovic, Prime Minister Zoran Milanovic and the war veterans minister at the Operation Storm anniversary "give hope that it will soon be possible to celebrate the victory in the war and the liberation of occupied parts of Croatia, while at the same time recognising the suffering and paying tribute to the civilian victims on 'the other side'."