One other who tried to escape via the same route after clashes with demonstrators Sunday was still missing, and a search was under way.
Soldiers said they came under attack from people armed with slingshots and sticks at a demonstration against the government of President Dina Boluarte in the city of Ilave in the Puno region.
Puno has been the epicenter of demonstrations that first broke out in December when then-president Pedro Castillo was ousted and arrested after trying to dissolve parliament and rule by decree.
His supporters are demanding the resignation of Boluarte, fresh elections, a new constitution and the dissolution of parliament.
More than 50 people have died and over 1,300 have been injured -- nearly half of them members of the security forces -- in clashes since then, according to the country's rights ombudsman.
The latest victims, the five soldiers, were identified by the military Monday as Franz Canazas, Alex Quispe Serrano, Elvis Pari, Elias Lupaca and Percy Castillo.
Their bodies were retrieved from the Ilave River, a tributary to Lake Titicaca on the border between Peru and Bolivia.
In a video distributed by the ministry, a soldier who managed to escape said he and his colleagues "crossed the river... because we had no other way out."
"Between 800 and 900 people surrounded us and started throwing stones at us," he said, seated among about a dozen other servicemen, all wrapped in blankets.
"People called us corrupt and murderers."
The soldier said the men had tried to form a human chain, but "the current took us, and... some of the troops began to drown."
A healthcare group in Puno said on Sunday it had treated five soldiers for hypothermia after local residents rescued them from the river.
On Saturday, 16 people -- civilians and soldiers -- were injured in clashes elsewhere in Puno that also saw a police station burned.
Castillo, 53, is serving 18 months of pre-trial detention in Lima, accused of rebellion. He was under investigation on several counts of corruption.
The demonstrations are driven by poor southern Indigenous Peruvians who see Castillo -- who is also from humble origins and has Indigenous roots -- as an ally in their fight against poverty, racism and inequality.
Elected for a five-year term, Castillo had been in office for only 17 months when he was dismissed.
He was the fifth Peruvian president since 2018 to be successfully impeached before the end of his term.
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