The ban also applies to using other messaging apps like Signal and Telegram on soldiers' private phones during service operations.
At the end of December, commanders and chiefs of staff received an email from headquarters recommending that their troops switch to using the Swiss-based Threema.
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The recommendation applies "to everyone", including conscripts doing their military service and those returning for refresher courses, army spokesman Daniel Reist told AFP.
Switzerland is famously neutral.
However, its long-standing position is one of armed neutrality and the landlocked European country has mandatory conscription for men.
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The question of using messaging apps on duty came up during operations to support hospitals and the vaccination programme in Switzerland's efforts to control the Covid-19 pandemic, Reist said.
The Swiss army will cover the four Swiss francs ($4.35, 3.85 euros) cost of downloading Threema, which is already used by other public bodies in Switzerland.
Other messaging services such as WhatsApp are subject to the US Cloud Act, which allows the United States authorities to access data held by US operators, even if it is held on servers outside the country.
Threema, which claims 10 million users, says it is an instant messenger designed to generate as little user data as possible.
It is not financed by advertising. "All communication is end-to-end encrypted, and the app is open source," the company says on its website.
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