The crackdown comes ahead of the East African country's Independence Day on Friday.
Release International, which supports persecuted Christians around the world, said it has been told by its contacts that streets are filled with police and secret police that are trying to prevent protests.
In 2002, Eritrea outlawed many Christian denominations and shut down Evangelical and Pentecostal churches.
Christians who worship in unregistered churches can face punishment and any believers in the armed services caught practising can be imprisoned.
Dawit, an Eritrean refugee, described how he was tortured to the Christian charity: 'I was arrested because of my Christian faith.
"Each night I had to sleep on the floor with my arms and feet tied together tightly, they called it the 'Number 8'."
Estimates vary to how many Christian prisoners are being held in Eritrea, as the authorities do not release records.
Most are believed to be Pentecostal or Evangelical and many have been held for more than a decade.
The recently arrested Christians, which includes 14 children, are believed to be in Adi Abeito prison, close to where they were arrested.
Release partner Dr Berhane Asmelash was tortured in Eritrea but said Christians inside the country are growing bolder as the Eritrean diaspora becomes more vocal in calling for greater religious freedom.
"People used to live in fear but since last July, people started to speak openly in the diaspora," he said in a statement.
Paul Robinson, Release International's CEO called for prayer.
"Things have to change in Eritrea.
"The country is no longer at war, but it still behaves as though it is - and the enemy is its own people.
"Release has long been campaigning for Eritrea to release its prisoners of faith and to grant freedom of worship. Please continue to pray for a radical change of heart in President Isaias Afwerki and his government, amid mounting international pressure for reform.
'It's time for the repression to end and for freedom to prevail'."
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