A Brazilian judge has banned a group of Christian missionaries from entering a vast Amazon indigenous reserve with the world’s highest concentration of isolated tribes, citing risks from the coronavirus pandemic as one of his reasons.

Indigenous leaders and activists hailed the decision as “historic” and expressed hope that it could prevent a genocide in the Javari valley, a remote reserve the size of Austria on Brazil’s western borders.

“Facing with this new coronavirus pandemic we wanted to guarantee the rights of indigenous people to isolation,” said Eliesio Marubo, an indigenous lawyer who sought the ruling on behalf of Javari’s indigenous association Univaja.

Federal judge Fabiano Verli banned three missionaries, Andrew Tonkin, Josiah McIntyre and Pastor Wilson de Benjamin, from the reserve, along with the controversial missionary group New Tribes Mission of Brazil which recently bought a helicopter to convert isolated peoples in the region.

The judge referred to recent articles about isolated groups’ vulnerability to common diseases that decimated their populations in the past and authorised police and army to expel any of the missionaries found in the reserve. Brazil has so far seen three confirmed Covid-19 deaths among its indigenous population.

Specialists from the indigenous agency Funai believe 16 isolated groups could live in the Javari valley. Concerns for their safety soared when a former New Tribes missionary was put in charge of Funai’s isolated indigenous department.

Verli wrote that Tonkin, a North American missionary, had been seen in the reserve and noted “clear indications of an attempt at cultural assimilation” of an isolated group.

Brazil’s O Globo newspaper said Tonkin was seen last year trying to make contact with an isolated group from the Korubo tribe using a hydroplane and was preparing a new expedition. Tonkin told O Globo the accusation was “gossip”.

New Tribes Mission said the group had removed all its missionaries from indigenous reserves by 23 March and “does not work with isolated peoples”. Funai said Brazil’s attorney general’s office would analyse the ruling.

“Every time that rights are threatened in the Javari valley we will go to court,” said Beto Marubo, an indigenous leader from the reserve.