Any official in Bosnia who fails to implement a decision of the international High Representative or obstruct it in any way can be jailed for from six months to five years under rules brought in to prevent the country sliding back to war.
Dodik has moved to separate the Serb-dominated region from Bosnia over the past two years and repeatedly criticised his political opponents and Western ambassadors to the country, where around 100,000 people died in a 1992-5 conflict.
The Serb leader, who has close ties with Russia, last month signed two laws that the peace envoy, German ex-government minister Christian Schmidt, had revoked saying they defied Bosnia's constitution and the terms of the peace deal.
One law suspended rulings by Bosnia's constitutional court and the second ended publication of the peace envoy's decrees and laws in the Serb Republic's official gazette. The state prosecutor said gazette director Milos Lukic was also charged.
"The prosecution of Bosnia-Herzegovina indicted Milorad Dodik and Milos Lukic for the criminal act of failing to execute the decisions of the High Representative," the prosecutor's office said, adding that the charges had been sent to the state court for confirmation.
Dodik, who is president of Bosnia's Serb Republic, has long advocated the secession of the Serb-dominated region from Bosnia, in which it coexists with a federation shared by Bosniaks and Croats under the country's 1995 U.S.-backed peace deal. His office rejected the indictement.
"The Republika Srpska (RS) President is indicted because he has obeyed the explicit provisions of the RS constitution and did not allow anyone and anything to rise above the RS constitution and its institutions, particularly not the decree of an unelected foreigner without legitimacy," Dodik's office told the Serb news agency Srna.
(Reporting by Daria Sito-Sucic; Editing by Philippa Fletcher)
By Daria Sito-Sucic
