Christian Solidarity Worldwide (CSW) has released a new report which claims there was a ten-fold increase in violations of freedom of religion or belief last year, with 2,300 cases.
The organisation, which promotes religious freedom, says church-goers in Cuba being arrested and dragged away on a weekly basis.
Speaking on Premier's News Hour, Kiri Kankhwende from CSW said: "The Cuban government is trying to perhaps limit the potential for social upheaval by cracking down on civil society.
"The church, after the revolution and after the repressive measures enacted against civil society as a whole, is one of the few places where people come together.
"As the government's trying to retain control, Christians are also starting to push back a bit a back.
"They're trying to resist in a peaceful, non-violent manner and we think that the government's trying to assert itself."
CSW says the rise in violations of religious or belief freedoms last year was largely due to the Cuban government declaring 2,000 Assemblies of God (AoG) churches illegal.
It's also claimed the state has also ordered the closure or demolition of AoG churches.
The group's report says the "consistently antagonistic relationship" between the Cuban Communist Party's Office of Religious Affairs, which oversees religious affairs on the island-nation, and the leaders of many religious group, "is evidence that the office exists solely to monitor, hinder and restrict the activities of religious groups."
Through the Office of Religious Affairs and other agencies, the government is being accused of continuing to refuse authorisation for numerous religious activities, issuing fines and making threats to confiscate dozens of churches and religious organisations.
CSW's report also highlights "more brutal and public tactics" being employed by "government agents" than were witnessed in the first decade of the millennium:
"Week after week, state security agents physically and violently dragged scores of women away from Sunday morning services.
"Most were arbitrarily detained until after the conclusion of religious services.
"The government continued to employ a strategy of frequent, temporary arbitrary detention to target those it views as political dissidents.
This tactic is also applied to religious leaders who are viewed as problematic, for whatever reason, by the authorities for the first time in four years a church leader was sentenced to and served six months in prison for holding unauthorised religious services."
Speaking about the report, CSW's Chief Executive Mervyn Thomas said: "CSW doesn't use the word 'unprecedented' lightly to refer to violations of freedom of religion or belief in Cuba in 2015.
"Following an upward trend in violations in recent years, 2015 witnessed a spike as the authorities deployed ever more public and brutal tactics to target churches across the denominational spectrum, regardless of their legal status.
"It is clear that despite promises of reform, the government is determined to maintain a tight grip on civil society, including churches.
"We commend the courage of religious groups who have spoken out publicly to denounce these violations and to call for the right to freedom of religion or belief to be upheld.
"We urge the international community to stand with them and to hold Cuba to account for these human rights violations."
Watch one Cuban pastor - Barnado de Quesada - being welcomed home after being released from detention.