BERLIN—BioNTech SE, the German biotech company that with Pfizer Inc. developed the first Western Covid-19 shot, unveiled mobile vaccine production units that it aims to deploy across Africa and other regions that have had limited access to supplies.

The modular factories, encased in shipping containers, will produce so-called messenger RNA vaccines and operate on a not-for-profit basis in developing countries, the company said Wednesday. Each unit, comprising 12 containers, can produce around 50 million doses a year.

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BERLIN— BioNTech SE, the German biotech company that with Pfizer Inc. developed the first Western Covid-19 shot, unveiled mobile vaccine production units that it aims to deploy across Africa and other regions that have had limited access to supplies.

The modular factories, encased in shipping containers, will produce so-called messenger RNA vaccines and operate on a not-for-profit basis in developing countries, the company said Wednesday. Each unit, comprising 12 containers, can produce around 50 million doses a year.

The modules can be transported by air, sea, road or rail and will be able to produce future mRNA-based vaccines to be developed by BioNTech, including shots for malaria and tuberculosis, as well as cancer treatments currently in clinical trials.

The cost of the development, manufacturing and shipment of the factories will be covered by BioNTech. The company declined to put a figure on the overall cost.

BioNTech said the development of the factories could boost medicine making for poorer communities by providing access to shots to remote or underdeveloped regions across the globe.

Mass production of vaccines and other medicines is currently dependent on sophisticated manufacturing hubs, most of which are based in industrialized nations. During the pandemic, developing countries have faced an acute shortage of vaccines as rich governments have snapped up the bulk of the global supply.

BioNTech and other vaccine makers came under criticism last year for refusing to hand over their patents to generic drugmakers in developing countries. BioNTech said at the time that waiving patents wouldn’t help the global vaccine crunch and instead pledged to set up local production facilities in countries lacking supplies and make doses available for free.

Pfizer, BioNTech’s global partner, isn’t involved in the project, the German company said.

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The two companies pledged last year to supply around two billion Covid-19 shots to low-income countries at cost by the end of 2022.

A Pfizer spokeswoman didn’t answer a question about why the company wasn’t participating in this effort and said it was working to boost its manufacturing capacity and partnering with manufacturers around the world.

BioNTech unveiled the production units, known as BioNTainers, on Wednesday at one of its factories in Marburg, Germany, in the presence of the leaders of Senegal and Rwanda, which will host the first modules, as well as Ghana, which will assist the initiative. Tedros Adhanom Ghebreyesus, the head of the World Health Organization, which supports the project, also attended.

“BioNTech’s innovative modular production system opens up a new horizon for global vaccine equity,” Rwandan President Paul Kagame said in a statement. Ghanaian President Nana Akufo-Addo said the project was a momentous step toward self-sufficiency of African vaccine production.

“We want to reach a new form of sustainability: not only to supply doses to low-income countries but to give people on the African continent the capacity to produce them for the African continent,” said Uğur Şahin, chief executive of BioNTech.

The container factories will be shipped in the second half of this year to Africa, where they will undergo a process of testing and regulatory authorization that could take over a year.

“The vaccine will be delivered (to Africa) in exactly the same quality that we have today in our production hubs,” Dr. Sahin said.

The final step of the vaccine-making process, known as fill and finish, involves packaging the doses into ampuls and will be carried out by local partners. The operation of the container factories will include technology transfer that will eventually see the production managed solely by local authorities.

Dr. Sahin said the first factories that will be shipped in the coming months would become the foundation of a future African end-to-end manufacturing network.

Production in Africa and elsewhere will, however, still depend on Western supply of key components. The vaccine developed by BioNTech and Pfizer uses 280 components from 86 suppliers in 19 countries; its production requires 50,000 different steps and 40 quality controls for each batch of shots.

Thomas J. Bollyky, at the Council on Foreign Relations, a U.S. think tank, welcomed BioNTech’s new initiative as an important step toward improving supply to developing nations, but said more had to be done by the global community given the volume needed to vaccinate vast populations across Africa and elsewhere.

“I think module vaccine manufacturing units are absolutely an important part of the solution to achieve more supply around the world, but I don’t think it’s a full substitute for local production… We’re still in a situation where, some 15 months into the vaccine rollout, low income countries have not been able to vaccinate 10% of the populations.”

About 75 people, including a team of five highly skilled experts, are needed to operate one container factory. Initially, the staff will be provided by BioNTech, which is already training African scientists who would operate the facilities. BioNTech will also run remote support for the factories around the clock in the initial phase.

—Jared S. Hopkins contributed to this article.

Write to Bojan Pancevski at bojan.pancevski@wsj.com