The Northern Marianas Descent Corporation says the US has proposed to use "the entire island with a full spectrum of weapons and joint training activities".
Claiming to represent over 7,000 indigenous people in the islands, the group has adopted a resolution that opposes the use of Pagan for military purposes.
The group's president, Ana S Teregeyo, has told Pacific Beat they felt the need to stand up against US military in order to protect the ancestral land of the indigenous Chamorro and Carolinian people.
"We took it upon ourselves to reply in accordance with... the most alarming statement regarding Pagan Island," she said.
The group accuses the US military of being secretive about their plans and the harm it may do.
"Pagan Island was never mentioned in the original negotiation between the US and the CNMI government...it has never been used for military purposes before," Ms Teregeyo said.
The group does not oppose to the US Department of Defense's use of Tinian Island that had been mentioned in the original agreement.
"We do not object to the military usage of other islands for the simple purpose of defending the US Constitution with regards to international or domestic defence," she said
"However, we do not intend to allow the use of Pagan because of its pristine surroundings."
The population of Pagan relocated to Saipan after a volcanic eruption in 1981.
"The people...that were relocated to Saipan want to go back but they're just waiting for the message from the government to return," Ms Teregeyo said.