The incident is reported to have taken place last month in the Jarvai Valley, the country's second-largest indigenous reserve which is home to an estimated 20 out of 103 uncontacted tribes registered in Brazil.
While agency workers say there is substantial evidence that an attack took place, it could take some time to confirm the incident in the very remote region.
Survival International told the Times that, due to the small size of most of these tribes, it is likely a significant proportion of their population has been wiped out.
Funai accused the government of letting down indigenous groups by slashing funding to their agency, forcing them to close guard posts and cut staff.
This is not the first time that tribes have come under attack from outsiders.
Back in 2011 an entire tribe went missing after heavily-armed drug dealers managed to overrun a Funai outpost.
Agency workers later apprehended the smugglers and found a broken arrow in one of their backpacks, prompting fears that the tribe was wiped out.
Brazil has a policy of not contacting such tribes but working to prevent the invasion of their land to preserve their autonomy.