The head of Brazil's indigenous protection service is to make an emergency visit to a remote jungle outpost, amid fears that members of an isolated Amazon tribe may have been "massacred" by drug traffickers.

Fears for the tribe's wellbeing have been escalating since late July when a group of heavily armed Peruvian traffickers reportedly invaded its land, triggering a crisis in the remote border region between Brazil and Peru.

On 5 August Brazilian federal police launched an operation in the region, arresting Joaquim Antônio Custódio Fadista, a Portuguese man alleged to have been operating as a cocaine trafficker.

But after the police pulled out, officers with the indigenous protection service (Funai) decided to return fearing a "massacre". They claimed that groups of men with rifles and machine guns were still at large in the rainforest. Reports suggest the traffickers may have been attempting to set up new smuggling routes, running through the tribe's land.

"We decided to come back here because we believed that these guys may be massacring the isolated [tribe]," Carlos Travassos, the head of Brazil's department for isolated indigenous peoples, told the Brazilian news website IG.

"We are more worried than ever. The situation could be one of the greatest blows we have seen to the work to protect isolated Indians in decades. A catastrophe … genocide!"

In an interview with the Globo Natureza website, the Funai co-ordinator for isolated groups, Antenor Vaz, said: "Either these guys have killed the isolated Indians or they have had contact with them. We know that these Indians defend themselves by attacking."

Facing mounting pressure, Funai's president, Márcio Meira, is on Tuesday expected to fly into a jungle position used to monitor the wellbeing of the area's indigenous people. The post is located about 23km (14 miles) from the Peruvian border and 240km from the already remote town of Feijo in Acre state.

The region made global headlines in 2008, when Funai released a series of startling aerial photographs proving the existence of never-contacted tribes there. The images showed tribesmen in one village, painted in red and pointing bows and arrows at a government aeroplane.

Earlier this year Fabricio Amorim, another Funai co-ordinator, said the region was home to "the greatest concentration of isolated groups in the Amazon and the world", though he added that illegal logging and drug trafficking represented major threats to such communities.

"We are extremely worried about this situation," said Fiona Watson, Brazil campaigner for Survival International. "It really highlights how out of control things are on the Peru side, and the urgent need for constant, long-term protection for the uncontacted tribes on both sides of the border."

She added that the situation was "potentially life threatening" for those communities.

José Carlos Meirelles, a veteran indigenous protection officer who is among the five-strong team of activists in the region, vowed to remain until action was taken.

"Since nobody from the Brazilian state is prepared to stay here, we took the decision… to come here," he wrote in one email to the media.

"We are completely surrounded," wrote Travassos. "We have nowhere to run. And we will not [run] until something is done."