Police detained electrical engineer Roberto David Castillo Mejia "as the intellectual perpetrator" behind Caceres's murder, the prosecutor's office said in a statement Friday.
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Officials said Castillo had served as CEO of the company Desarrollos Energeticos (DESA) -- which Caceres actively campaigned against over plans to build a hydroelectric dam -- at the time of the activist's slaying.
He was "responsible for providing logistics and other resources to the perpetrators," the statement said.
Caceres opposed DESA's plans to construct the dam across a river on which indigenous communities depended.
Two masked gunmen fatally shot the activist at her home in La Esperanza, northwest of the capital Tegucigalpa on March 3, 2016.
Her murder sparked international outrage and highlighted threats to Honduran activists.
At least eight other people have been arrested in connection with the homicide -- among them employees of DESA -- but Caceres' family has repeatedly demanded the masterminds be brought to justice.
Late Friday some 400 people including relatives and members of the indigenous community in western Honduras marched to reiterate that call.
Caceres "taught us to defend the river, the land and the forest -- we are not going to surrender," said Lenca Paulina Gomez as she rallied marchers over a loudspeaker along the main street of La Esperanza.
In a statement issued after his arrest, DESA said "Castillo, like all members of DESA, are totally dissociated from the unfortunate incident that ended the life of Ms Berta Caceres."
"We respectfully request the immediate release of Mr David Castillo," said the company, whose dam project has been suspended but not canceled.
The Honduras branch of the UN High Commissioner for Human Rights on Twitter said it "continues to express its support for the family" of Caceres and "efforts to seek the truth".
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