Authorities in Rio de Janeiro and several other Brazilian cities have said they would pause some coronavirus jabs because of a shortage of vaccines, as supply bottlenecks threaten to slow the inoculation programme in Latin America’s largest nation.

A number of municipalities including Rio, home to 6.7m people, have in recent days paused first injections — or said they intend to — because of a lack of supply, with priority given to those waiting for a second shot. Salvador, home to almost 3m residents, has suspended first vaccine doses for health workers and the elderly.

“We are waiting for a new delivery from the federal government so we can proceed with the vaccination schedule in our city,” Bruno Reis, Salvador’s mayor, tweeted this week.

Globo, the Brazilian broadcaster, reported that at least five cities had part-suspended vaccinations or planned to do so in the coming days. The vaccination rollout will continue in the country’s most populous city, São Paulo.

The shortages follow delays in imports of vital pharmaceutical ingredients from China, which have pushed back the production schedules of domestic laboratories supplying the vaccines. Government officials say they expected all states to receive further vaccine batches next week, underpinning hopes of a quick restart.

Brazil’s inoculation campaign kicked off a month ago, behind a number of other Latin American countries and following political infighting that has marred its response to the pandemic. Some 5.5m people have received at least one dose, according to local media estimates, about 2.6 per cent of the population of 213m.

However, there have been accusations of queue-jumping and reports of patients receiving fake vaccines, as well as questions over who is given priority.

Brasília is far from alone in coming up against vaccine availability issues. The EU and countries including Mexico and Canada have also run into problems.

But critics of president Jair Bolsonaro’s administration say this is just the latest instance of mismanagement during the Covid-19 crisis. The rightwing populist has played down the severity of the disease and vowed not to take a jab himself after recovering from the virus.

While Brazil’s Covid-19 death toll of almost 250,000 is the second-highest in the world after the US, it is ranked 24th on a per capita basis, behind several western nations and regional neighbours.

The health ministry said it had contracts for 365m vaccine doses, after signing for an additional 54m vials of the Chinese-developed CoronaVac, the country’s main bet alongside the Oxford-AstraZeneca shot.

It also hopes to conclude a deal for 10m doses of the Russian Sputnik V vaccine. At no time had the federal government “been absent or abstained from its responsibilities”, the department added.

However, the National Confederation of Municipalities, a local government association, said attempts to open dialogue with the health ministry had been ignored. It called for the removal of Eduardo Pazuello, health minister, who is under scrutiny after oxygen supplies ran out in the Amazonian city of Manaus last month as its hospital service was overwhelmed.

Fernando Aith, professor of public health at University of São Paulo, said: “We are running a serious risk of losing all this vaccine that has already been given, because of not having the second dose, as well as guaranteeing the immunisation that tests showed would be effective”.

Additional reporting by Carolina Pulice in São Paulo