Government security officers are said to have removed the staff from the health centers and closed them.
Patients were ordered to go home and soldiers were deployed to guard the centers, the bishops said in a June 13 letter to the ministry of health. The church runs more than 20 clinics in Eritrea, and many are on the property of monasteries.
In their letter, the bishops said the services the church provides to Eritreans could not be construed as an act of opposing the government. The church's main concern is the people in need of the services that the government action has halted, it said.
In a May interview with Catholic News Service in Nairobi, an Eritrean Catholic nun said the government has some control over the church in the country and that it is a "closed" church.
"We are subjected to looking over our shoulders to serve the people" of Eritrea, she said, noting that the freedom the church has in other countries "is not with us."
The sister, who was attended a meeting in the Kenyan capital organized by the Association of Member Episcopal Conferences in Eastern Africa, known as AMECEA, asked not to be named.
"Our relations with" the church in other countries, including those in the region, "as well as our pastoral operations are somewhat government controlled," she said.
Before the seizure, government officials were said to have asked administrators at the church-run facilities to sign a document approving the handover. Most are said to have refused.
"The government can say it doesn't want the services of the church but asking for the property is not right," the bishops' letter said.
In April, Eritrea's bishops called for a truth and reconciliation plan to be set up and said perpetrators need to admit their crimes.
In July 2018, Eritrean President Isaias Afwerki and Ethiopian Prime Minister Abiy Ahmed signed a peace pact in the Eritrean capital, Asmara, to bring an end to the two-decade war between the East African countries. An estimated 80,000 people are believed to have been killed between 1998 and 2000 during a fierce border conflict. However, after the two countries signed a U.N.-brokered border agreement in 2000, they failed to implement it.
Because of war and related factors, "the living conditions of our people" have reached critical levels and "massive fleeing abroad continues," the bishops said in their April pastoral letter.
Hundreds of thousands of people have fled Eritrea in recent years, with many making perilous journeys through deserts and across the Mediterranean Sea to Europe.