The church, named Sanjiang, is located in Ou Bei township in Wenzhou, which is home to one of China's largest Christian communities.
The protest started on March 25 after authorities said the government-approved Protestant church had illegal structures and additions that violated building codes.
The stand-off took on an increased urgency on April 3 when pastors affiliated with the church were notified that authorities planned to demolish the building within 15 days.
The campaign to save the church moved into its 13th day with congregants and pastors holding sit-ins around the clock.
Church leaders led the congregation on a march on Saturday, gathering in front the church, while a prayer vigil took place inside.
Police set up roadblocks at the scene. Uniformed police and plainclothes security agents were present, according to several church members.
"We are not seeking a violent confrontation," said a protester who identified herself as a Christian from neighbouring Longgang township. "We are holding a peaceful sit-in, praying to God for help."
While crackdowns on unauthorised "home churches" are fairly common on the mainland, the newly constructed Sanjiang church, which worshippers said cost 30 million yuan (HK$37 million), was government-approved, operating under the auspices of the Three-Self Patriotic Church.
According to the Wenzhou government website, Sanjiang church was designated a "model project" on September 16.
Members of the Sanjiang congregation believe their church was targeted after Xia Baolong , the Zhejiang party secretary, visited the region and was troubled by the size of the building - an eight-storey structure covering more than 1,000 square metres.
By Friday afternoon, several church pastors had reached a verbal agreement with local authorities to tear down a teaching annex but save the main building, which is topped with a large cross.
Some pastors opposed the agreement.
"The main building and the annex are integrated for a reason," said one of the pastors, who refused to give his name, fearing reprisal.
"We are also concerned about the lack of a written agreement".
The stand-off comes amid signs of a wider crackdown on churches in Wenzhou, an affluent city in southeast Zhejiang.
Local churchgoers said similar demolition notices were sent to churches in three other Zhejiang townships - Taishun , Wencheng and Ruian .
A churchgoer from Yuyao township in Hangzhou said officials were targeting churches in the region - especially those with prominent religious symbols, such as crosses.
"They said the holy cross was built too high and violated the building code," said Timothy Liao, a priest from Wenzhou. "But why only target churches when many buildings violate height limits? Clearly, this is a pretext to tear down churches."
About 1,800 people attend regular services at Sanjiang. The number was expected to rise to as many as 4,000 once the planned expansion of the church was completed.