Global Witness says 123 people have been killed protecting their land in Honduras since the 2009 coup.
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."
The report criticizes the United States for "backing Honduran state forces, which are often behind the murders and attacks of activists." The United States is Honduras' main trading partner, according to the State Department.
In 2013, the two countries had a $9.8 billion trading partnership.
In response to the report, the United States asserted its commitment to addressing human rights concerns in Honduras.
"The United States is focused on supporting Honduran efforts to address impunity, strengthen civil society, and create conditions that will bring about security and broad-based economic prosperity for Hondurans," a spokesperson for the State Department told CNN, noting the US Embassy's recent $2.9 million pledge
to Freedom House, an organization that works with the Honduran government to help protect human rights defenders.
Arrests made in death of environmentalist
The Honduran government has repeatedly said it works hard so those responsible for the crimes are brought to justice, and to ensure that the most vulnerable groups are not bothered or attacked.
In Cáceres' case, seven people have been arrested in connection to her death, including the man who managed the Agua Zarca dam project for Desarrollos Energeticos.
"We have to denounce who designed the crime, who planned it, who paid for it, and also the people inside the company who promoted the harassment, prosecution, criminalization that lead to her being murdered," Cáceres' daughter, Berta Zuniga Cáceres, told CNN en Español.
The company denies involvement in the killing or any wrongdoing.
Meanwhile, Silvio Carrillo, Berta Cáceres' nephew, is pushing for a bill in the US Congress -- the "Berta Cáceres Human Rights in Honduras Act
" -- that would cut all security funding for Honduras until "human rights violations by Honduran security forces cease and their perpetrators are brought to justice."
"This is not just about Berta," Carrillo told CNN. "She may have been simply collateral damage to the US government, but to us and the millions who support us around the world, she -- and the at least 123 other dead activists -- are a symbol of a US policy that has clearly failed. We continue to ask that the US stop supporting this criminal syndicate that claims to be a government in Honduras."