Revd Jesús Noel Carballeda, 45, was detained in early February and imprisoned in the Valle Grande prison in San Antonio de los Baños outside of Havana.
Christian Solidarity Worldwide (CSW) have said he was never tried, but while in prison he was informed by government officials that he would be held for six months as punishment for his continued unauthorised religious activity.
Reverend Carballeda's church is linked to the Apostolic Movement, a fast growing network of protestant churches which the Cuban government has refused to register. Because the religious group is unregistered, all of the affiliated church's activities are technically illegal and they are unable to apply for permits for a designated place of worship.
In March, Reverend Carballeda's wife told CSW: "We do not want to bother anyone. We just need a place to worship. We are forced to meet in the open air, in parks or rented rooms as [the authorities] will not give us legal recognition."
Activists say the the detention of Reverend Carballeda is part of a larger crackdown on religious freedom in Cuba over the past few years.
In 2014, CSW documented 220 separate cases of religious freedom violations, up from 185 in 2013 and 120 in 2012. Unregistered religious groups have been a particular target of government repression, with religious leaders reporting harassment, fines and threats of confiscation or destruction of property.
CSW's Special Ambassador Stuart Windsor said, "While we welcome the release of Reverend Carballeda, we note that he was only released after serving a full six-month sentence for the supposed crime of holding unauthorised peaceful religious services.
"As Cuba prepares for the visit of the Pope this month, we continue to call on the Cuban government to bring legal matters related to religious activities and groups under regular legal mechanisms and remove the Office of Religious Affairs from its position of authority over all religious groups and activities.
"We urge the government to cease its harassment of all religious groups, both registered and unregistered, and to allow religious groups who wish to register and to operate legally to do so."