The sentences set off weeks of protests in the northeastern region, at times erupting in violent clashes that saw projectiles fired, cars torched and barricades set alight in the regional capital of Barcelona.
"It is clear that the Supreme Court's interpretation of the crime of sedition was overly broad and resulted in criminalising legitimate acts of protest," said Daniel Joloy, a senior policy advisor with Amnesty International.
The report homed in on the cases of Jordi Sanchez and Jordi Cuixart, two rights activists who were sentenced to nine years in prison for ignoring court orders by leading a protest against a police operation designed to halt the referendum.
As private citizens and the leaders of civil society organisations, both men had the right to express their opinions and organise peaceful meetings to support the push for independence in Catalonia, the organisation said.
The other jailed separatist leaders were politicians rather than rights activists. The statement published by Amnesty International did not spell out in details the group's views on what should happen to them.
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