The Cairo studios of Christian satellite broadcaster SAT-7 were raided on Saturday by officers of Egypt's Censorship Department who accused it of operating without the necessary licences.
Items of equipment including cameras and computers used for editing were confiscated and the office director, Farid Samir, was detained for six hours before being released, SAT-7 said.
He faces four charges relating to operating a satellite TV channel without the correct licences.
However, according to SAT-7, the Egypt office is a programme production facility and not a satellite broadcast centre. It said that all the charges were "based on a lack of and/or incorrect information".
A decision will be taken by the Public Prosecutor in the next few days about whether the case will go to court. In the meantime SAT-7's activities in Egypt are severely disrupted, though broadcasts to Egypt are continuing from Beirut.
The president of SAT-7 USA, Rex Rogers, said: "As far as we know, we've done absolutely nothing wrong. We have the appropriate licensures and approvals. This is a misunderstanding, but unfortunately, it could cost us."
SAT-7's work in Egypt is carried out under the legal umbrella of the Coptic Evangelical Church but its services are in support of all the Church denominations in the country.
After Sunday's court hearing, Samir asked Christians to "unite with us in prayer so that we can complete our ministry – one based on love and which aims to serve our beloved country".
The issue of censorship is of increasing concern among Egyptian media following the passing of a new anti-terrorism law in the summer. Christians are a minority in the country and face continual pressure from Muslim hard-liners, though the country's President Abdel Fattah el-Sisi has strongly urged tolerance and religious freedom.