The decision was taken after a meeting with President Charles Taylor to discuss accusations made against the head of the Catholic Church, Archbishop Michael Francis.
The Reverend Pelessant Harris, secretary general of the Liberian Council of Churches said that President Taylor had promised to bring the parties to the current dispute together, to examine the evidence over claims made.
"I think very soon the whole issue will be resolved," he told the BBC's Network Africa.
Nuns
The church and the government have been trading accusations since Archbishop Francis launched an investigation last week into the murder of American nuns 10 years ago.
At the time fighters loyal to Mr Taylor were accused by the Archbishop and the United States of carrying out the killings.
A member of parliament - Sando Johnson responded by accusing the Archbishop of failing to address homosexuality in the Catholic Church.
Activities at all church-related health and learning institutions throughout the country were seriously disrupted on Monday - the first of three days of planned disruption.
Distanced
Archbishop Michael Francis has often criticised President Taylor's government saying it has a poor human rights record.
In a statement on Monday, the government urged church leaders to call off the protest in the interest of education and the health of the of Liberian people.
The government maintained that Sando Johnson's allegations against Bishop Francis were his personal views.
But the Council of Churches disagreed. It said that "when an official who holds such a high office speaks, he cannot separate himself from his office."
Mr Johnson has shown no regrets for his allegations despite mounting criticism.