A Bishop's house and church-run clinic were raided by over 200 soldiers and police in Kayah state on Monday.
Medical records were seized and 18 healthcare workers were arrested at Karuna clinic and Christ the King Cathedral compound in Loikaw, according to church officials.
Local sources say junta troops surrounded the Christ King Cathedral, blocking residents from entering.
40 patients, including four infected by the Covid-19 virus were also forcibly removed from the premises and relocated to the Loikaw People's Hospital.
The charity health clinic provides free medical services to locals of all religious and racial backgrounds.
The chancellor of Loikaw Diocese, Father Francis Soe Naing told UCA News: "We are carrying out charitable works and weren't involved in any wrongdoing. We have no idea why they raided us and what they searched for."
Following a coup in which the Myanmar military seized power in February 2021, violence towards believers and crackdowns on Christian institutions have intensified. There have been increasing reports of shootings and arrests of clergy, and buildings in Christian areas being burned.
Numerous parishes in Loikaw Diocese are reported to be affected by the recent conflict which has displaced some 100,000 people in the Catholic majority region.
Myanmar is number 18 on Open Doors' World Watch List, an annual ranking of the 50 countries where Christians face the most extreme persecution.
Christians make up eight per cent of Myanmar's population, according to Open Doors' World Watch Research.