Police officers and security agents blocked off roads in a bid to arrest Mario Felix Lleonart Barroso, a prominent pastor and religious freedom activist.
He was not at home but several church officials were detained to stop them protesting at the demolition of the churches.
Both churches belonged to the Apostolic Movement, an unregistered network of Protestant churches.
Government officials initiated the destruction of Revd Bernardo de Quesada Salomon's church, an open-air structure in Versalles, Camaguey, and that of Revd Juan Carlos Núñez Velázquez, in Victoria de las Tunas, without prior warning in the early hours of 8 January.
Anti-persecution charity Christian Solidarity Worldwide said state security agents broke down the door and handcuffed pastor Bernardo de Quesada Salomon and his wife Damaris, taking them to two separate prisons while the demolition took place.
They were released once the demolition had finished.
The charity said many church members had their phones cut off to prevent them from spreading the news about the demolition.
Cuba claimed both the churches were built without planning permission, but the pastors deny that.
Last year, 2,000 churches linked to the legally recognised Assemblies of God denomination were declared by the government to be illegal.
Meanwhile, 100 of those in just three provinces, Santiago, Guantanamo, and Contramaestre, were designated for demolition and forced closure.
Mervyn Thomas, Chief Executive of Christian Solidarity Worldwide (CSW) said: "We urge the international community to raise the demolition of these two churches, the detention of the pastors and the threats against others with the Cuban government as a matter of urgency.
"We are deeply concerned for the wellbeing of Reverends de Quesada Salomon and Núñez Velázquez and their families.
"Their treatment at the hands of the government is unacceptable and all restrictions on their freedom and communication must be lifted without delay.
"Contrary to the hopes of many that political dialogue with United States and the European Union would lead to more freedom in Cuba, over the past year we have seen a severe regression in terms of freedom of religion or belief and shrinking space for religious groups to operate.
"We 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."