Cuba has begun withdrawing 8,300 doctors working in some of the poorest regions of Brazil, prompting fears that indigenous villages, small towns and isolated rural communities could soon be left without medical care.

The move came after Brazil’s far-right president-elect Jair Bolsonaro threatened to cut relations with Cuba and modify the conditions of a five-year-old agreement between the two countries and the World Health Organisation. The growing row offers a worrying sign of how the former army captain may handle diplomacy after assuming office on 1 January.

On Tuesday, Brazil published an emergency tender for doctors trained in the country to replace the Cubans who were working under a programme called Mais Medicos, or More Doctors.

Chartered flights have begun carrying the Cuban doctors home, some carrying televisions and other goods, causing queues and cancelled appointments where they worked. Medical experts are worried the government will be unable to fill all the vacancies before they have all left by WHO’s expected final date of 12 December.

“I am extremely concerned about the potential health impact of this and how Brazil will be able to fill those positions,” said Albert Ko, a professor of epidemiology at the Yale School of Public Health who has worked in Brazil.

The result will be “an abrupt fall in medical attention,” said Henrique Passos, a medical supervisor for Cuban doctors working in far-flung indigenous communities in the Amazon, many of which got their first doctor under More Doctors.

Cuba announced it was pulling out of the programme on 14 November, blaming Bolsonaro for declaring plans to modify the terms of the programme by insisting that Cuban doctors validate their diplomas and sign individual contracts. It also accused him of making “direct, contemptuous and threatening comments.”

Earlier in the month, Bolsonaro, had questioned whether Brazil could maintain diplomatic relations with Cuba and said the More Doctors could only continue if Cuban doctors validated their diplomas and received their full pay.

Currently, Cuba keeps around 75% of the doctors’ £2,400 allowance, though housing and food is paid by local authorities.

Cuban doctors Carlos Raul Lujos and Alioski Ramirez in Brasilia, Brazil. Leasing medical professionals is Cuba’s main export, bringing in more hard currency than tourism. Photograph: Adriano Machado/Reuters

Even so, for Cuban doctors, the experience can be life-changing.

Yanet Rosales Rojas, 30, spent three years working in the Brazilian town of Poços de Caldas, where on average she earned more than 10 times her monthly salary in Cuba. She returned to the island last year, and was able to buy an apartment in Havana.

“You earn much more than what you get in Cuba. I always wanted to travel and treat people in other countries. This was my chance,” she said.

Leasing medical professionals is Cuba’s main export, bringing in more hard currency than tourism: last year professional services by doctors and nurse brought in $11bn , compared to $3bn in tourism.

The chance to earn abroad is major incentive to study medicine, especially after a decade of private sector expansion where young Cubans have become less willing to work for the state.

Sending doctors abroad also helps Cuba project soft power: Cuban doctors are currently working in 67 countries, and Cuban medical teams are often at the forefront of disaster relief efforts in the region (where they work free of charge.)

In Brazil, more than 18,000 doctors have taken part and 63 million people benefitted, according to the country’s health ministry.

Bolsonaro has been fierce critic of the programme since it was introduced by leftist President Dilma Rousseff in 2013 – and he is not alone in his criticisms: when the first contingent arrived in Brazil in, they were booed by local doctors, and the Brazilian Medical Association has said the scheme left Brazil “submissive” to another country.

“We can’t allow Cuban slaves in Brazil and we can’t keep feeding the Cuban dictatorship,” Bolsonaro told reporters on Sunday.

But some of the Cuban doctors disagree with such criticisms.

“I don’t think it’s right the government kept most of the money but the Brazilian people are also slaves to high taxes,” said Cuban doctor, who talked via WhatsApp from an indigenous reserve on the condition his name was not revealed.

“We are in a cross fire between two political ideals,” said Hendry Jant, a Cuban doctor who visits isolated indigenous and riverside communities in the Amazon state of Pará for a floating health project called Saúde e Alegria – Health and Happiness. “We’re doctors not politicians.”

Ko said that Brazilian doctors were originally given priority when the programme launched; the Cubans came in after they failed to sign up. “Brazil produces a lot of medical doctors,” said Ko, “but where they work is distributed unequally … they attend the wealthier sectors of society rather than the poor.”

According to the Brazilian Association of Collective Health, in around 10% of municipalities the only doctors are Cuban. The program has resulted in “widened access and improved the quality of health attendance”, the Association said, a view backed up by several academic studies.

Carlos Lula, the health secretary of the dusty, Northeastern state of Maranhão, said that previous attempts to hire Brazilian doctors had floundered, adding that he feared the 471 Cuban doctors currently working there would be hard to replace.

Brazil’s President-elect Jair Bolsonaro said ‘More Doctors’ program could only continue only if Cuban doctors validated their diplomas and received their full pay. Photograph: Léo Corrêa/AP

“The impact will be terrible,” he said. “I have a big demand and a small supply of doctors.”

Some Cuban doctors have rebelled against the scheme. Around 150 have joined lawsuits against both governments and the WHO to stay in Brazil at the end of their assignments and receive the same money as Brazilian colleagues, said André Corrêa, a lawyer in the capital Brasília representing them. He has successfully represented five Cuban clients – three of whom are getting fully paid – and received a flurry of calls since last week’s announcement.

“We don’t believe there is one doctor who wants to get less than other doctors doing the same job,” Corrêa said.

One of his clients, Cuban doctor Yolexis Nodarse won an interim court decision to keep working in Brazil. “It’s difficult in Cuba,” she said, “so to help the family we go abroad.”

She would like to leave her “very small, very poor” town of Ponte Alta de Bom Jesus – population, 4,600 – deep in Brazil’s interior, but hopes to stay here. “It is well paid, the work conditions are good,” she said, unlike Cuba where “people are scared to talk because you could go to jail.”

Bolsonaro’s vice-president elect, General Hamilton Mourão, has suggested half of Brazil’s Cuban doctors will stay, but Caetano Scannavino, who founded the Health and Happiness programme, asked why Bolsonaro hadn’t drawn up a contingency plan or negotiated a peaceful transition.

“What matters is that these populations can’t end up without a doctor,” he said. “Cuba is not responsible for public health in Brazil. The government is.”