Anti-persecution charity Christian Solidarity Worldwide says it's found 220 separate incidents in the past 12 months.
Its research has found issues ranging from harassment and fines to confiscation and destructions of church property.
The charity says it's heard stories from various different denominations around the country, where church leaders or congregation members have been beaten and put in prison.
CSW's Chief Executive Mervyn Thomas said: "We were disappointed but not surprised to see another significant increase in religious freedom violations in Cuba, as it continues the trend of the past five years.
"Government promises of reform have not been reflected in the reality on the ground in Cuba. Raul Castro's government continues to maintain a tight grip on civil society and religious groups are not exempt.
"However, it is important to commend the courage of many religious leaders in Cuba, more and more of whom are speaking out publicly to denounce such violations and to call for religious freedom.
CSW's now calling on international governments to take action to stand with the victims and hold the Cuban government to account.
Mervyn Thomas said: "We call on the international community and in particular the United Kingdom, European Union and the United States Government, to stand with these brave leaders and to hold Cuba to account on religious freedom.
"Respect for fundamental human rights must be a part of any political dialogue and the cornerstone of any economic or political agreement."