The Catholic leader also appealed for peace in the Latin American nation, amid unrest first prompted in April by new legislation which cut social security and pensions.
The news agency of the Holy See, Vatican News, said: "Uniting himself to the concerns of the country's bishops, the Pope called for an end to all violence and prayed for the victims and their families."
Despite, swiftly revoking the unpopular law he introduced, President Daniel Ortega has seen himself become the focus of disquiet in Nicaragua - which is home to 5.9 million people.
Francis said that the Catholic Church is always supportive of dialogue but "it requires active engagement in respect for freedom and, above all, life."
Human rights campaigners have accused police of using excessive force against demonstrators.
President Ortega says he has no intention of quitting.
On Saturday, two people died when police laid siege to a church where approximately 30 opposition supporters sought refuge - 20km south of the capital Managua. They were later freed after Catholic authorities intervened.
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