One protester was killed and dozens of people were injured as police fired tear gas and the Christians threw stones and petrol bombs.
The Christians said they had permission to build the church, in Cairo##s Giza district, but officials said they did not have the proper permit.
Protests on this scale are rare from Egypt##s Christians. They make up about 10% of the country##s 85 million population.
There has been friction in the past between the majority Muslims and Christians, who complain they do not have the same freedom to build places of worship.
The interior ministry said more than 100 people had been arrested. A ring of police surrounded the church in order to prevent construction of the church and security was tight in the Giza suburb.
“People here feel very discriminated against. We can##t build the church – why are they stopping us?” said Samih Rashid. “Every street has a mosque, every church has a mosque next to it,” he told AFP news agency.
Some reports said the builders were trying to convert a Christian social centre into a church without the proper permit – something the Christians denied.
“When we noticed indications that it was turning into a church, we told the church authorities to halt construction because a church would require a different licence,” Giza governor Sayyed Abdel-Aziz was quoted as saying by Reuters news agency.
BBC World News