The office of President Juan Orlando Hernandez said the head of state "has today (Friday) accepted the resignation of the secretary for foreign affairs and international cooperation, Arturo Corrales."
Corrales was Orlando's security minister during an alleged cover-up of the police involvement, which came to light through recent reporting by the Honduran newspaper El Heraldo.
The daily cited a security ministry document revealing that senior police officers ordered the assassination of Honduras' top anti-drugs official, Aristides Gonzalez, in December 2009.
The hierarchy of the security ministry in place between 2009 and 2014 covered up the information, the newspaper said.
Corrales was security minister for one year, from January 2014 until January 2015, when he was made foreign minister.
Honduras' public ministry, which handles state prosecutions, opened an investigation last week after a raid on the police headquarters turned up evidence regarding Gonzalez's murder.
The president has asked Congress to approve an emergency decree aimed at accelerating a clean-up of the 12,000-strong police force that has been dragging on for four years now.
Authorities believe more than one in 10 of the officers is dirty and must be booted from the police force.
