Global Witness says 123 people have been killed protecting their land in Honduras since the 2009 coup.
The report comes nearly a year after award-winning environmentalist Berta Cáceres
was shot dead inside her home
after fighting against one of Central America's largest hydropower projects.
The two-year investigation sheds light on what the group says is political corruption within Honduras and some of the major players.
Gladis Aurora López, the president of the country's ruling party and vice president of Congress, is seen as "one of several top politicians and business tycoons implicated in a violent crackdown," the report said.
The report ties López's husband, Arnold Gustavo Castro, to the controversial hydroelectric dams, Los Encinos and La Aurora, which are being built on sacred indigenous lands. As the sole director of the companies behind the dams, Global Witness says he illegally obtained the contracts when his wife was in Congress.
Three indigenous activists who fought against Los Encinos dam were killed, "their bodies dismembered and showing signs of torture," Global Witness said.
López and her husband denied any involvement, according to Global Witness. They did not respond to CNN en Español's requests for comment.
Warnings against possible 'false accusations'
Others within the government caution against making such bold accusations.
"They have to be certain about the implication of the people they are bringing accusations to," warned Jorge Gallindo, a spokesman within the criminal investigation technical agency in Honduras. "Doing something prematurely can lead to false accusations or damage the investigation."
Honduras, a poor nation building itself up after the 2009 coup, has six out of 10 rural households living in extreme poverty on $2.50 per day.
The region, which has seen an unequal distribution in wealth and land, is "rich in resources, but high-level corruption and a weak rule of law contributes to the current situation for community leaders being killed in record numbers," Billy Kyte of Global Witness told CNN in an email.
He accuses the country's elite of using "corrupt and criminal means to cash in on the country's natural wealth, and are enlisting the support of state forces to murder and terrorize the communities who dare to stand in their way."
"Those who speak out are being silenced in record numbers," Kyte said. "These are ordinary people defending their lands against the illegal imposition of mining, hydrodams, agribusiness projects."