Security officers raided Faith Missions Church in Keren - Eritrea's second largest city - last Sunday, confiscating property they found in the building.
The raid comes just over a week after authorities seized 21 health facilities belonging to the Catholic Church and arrested five Orthodox priests.
The East African country has witnessed a clampdown on Christians in recent months.
More than 140 Christians in the capital Asmara were arrested in May while they were attending a private meeting.
Faith Missions Church is one of four religious communities still awaiting registration from the state despite claiming to have submitted the necessary documentation in 2002.
In May 2002, Eritrea introduced a registration policy that effectively outlawed all religious practices not affiliated with the Catholic, Evangelical Lutheran or Orthodox Christian denominations and Sunni Islam.
Eritrea's human rights record will be reviewed at the United Nations Human Rights Council (HRC) on 2nd July.
Christian Solidarity Worldwide's (CSW) chief executive Mervyn Thomas said in a statement: "CSW is deeply concerned by this latest development in a crackdown on people of faith in Eritrea that has been ongoing since 2002.
"We call for the immediate and unconditional release of all members of Faith Missions Church, as well as all other prisoners of conscience in the country."
"It is essential that UN member states seize the opportunity presented during next week's interactive dialogue at the HRC to raise these concerns. We also urge member states to support and facilitate the renewal of the Special Rapporteur's mandate in order to ensure continued monitoring of the dire human rights situation in Eritrea."
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