Emanuel Church, affiliated to the Apostolic Movement, an unregistered Protestant denomination, was demolished by the authorities earlier in the week and hundreds of church members were detained.
Revd Alain Toledano's church in Santiago de Cuba was surrounded by officials, including the police, state security and the military in the early hours of the morning on February 5th.
His wife, MarilÃn Alayo Correa, was also detained before both Emanuel Church and the pastoral home was destroyed.
The destruction of the church follows similar demolitions of two Apostolic Movement churches in Camaguey and Las Tunas provinces in January.
Anti-persecution charity, Christian Solidary Worldwide (CSW), has reported that around 200 leaders and members of Emanuel Church were also detained in the raid.
It is thought that around 40 people were held in a local school while others were taken to police stations across the region to stop them from protesting against the demolition.
Church leaders have also said some people were beaten while they were detained.
The property is privately owned by Revd Toledano and the government had approved the construction of and renovation work on the buildings but he said he received numerous threats of church eviction and closure in the past few months.
The government has refused to register the Apostolic Movement denomination on a number of occasions.
Revd Toledano was in the United States at a religious event when the government action against the church took place.
He told CSW he believes the Cuban government intentionally carried out the eviction and demolition when he was out of the country, and he added he was worried about his young daughters who saw their mothers being detained.
CSW's Chief Executive Mervyn Thomas said: "We are extremely disturbed to learn of this latest church demolition by the Cuban authorities, in a similar manner to the destruction of the two Apostolic Movement churches on 8 January.
"We are also extremely concerned for the family of Reverend Toledano and his wife MarilÃn, who saw their home razed as part of this destruction.
"This series of demolitions since the New Year indicates a worrying escalation in terms of violations of freedom of religion or belief in Cuba. Again, we urge the international community to raise the demolition of these three churches, the mass detentions of pastors and church members, as well as the threats against others with the Cuban government as a matter of urgency.
"We continue to call on the EU and the US to make freedom of religion or belief a central component of its dialogues with Cuba and to insist on improvement in this area."
