Juan Lopez, who campaigned against open-pit iron ore mining, was shot dead on September 14 after leaving church in the northeastern town of Tocoa.
"We've captured the material author of the death of environmental activist Juan Lopez. An accomplice was also arrested," Security Minister Gustavo Sanchez wrote on social media platform X, without giving their identities.
A motorcycle used in the attack was seized and more than one hundred videos were reviewed as part of the investigation, Sanchez said.
"Other raids are being carried out to also make another arrest," he added.
The detainees were Oscar Alexis Guardado Alvarenga, 27, and Lenin Adony Cruz Munguia, 30, said national police director Juan Manuel Aguilar in a press conference.
Days before his death, Lopez, 46, had called in a press conference for the resignation of the Tocoa mayor after he was caught on video negotiating bribes with drug traffickers in 2013.
The official denied involvement in the murder, which was denounced by the United Nations and Pope Francis.
In an interview with AFP in 2021, Lopez discussed the risks he said environmental activists face in the poor and violent Central American country.
"If you start defending common interests in this country," he said, "you clash with major interests."
"If you leave home, you always have in mind that you do not know what might happen, if you are going to return," said Lopez.
The Inter-American Commission on Human Rights had ordered protective measures for Lopez due to threats against him and other environmentalists from Tocoa.
According to the human rights group Global Witness, Honduras is one of the world's most dangerous countries for environmental activists.
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