"Six hundred people were inside the church when the blast took place," deputy commissioner Zaheerul Islam told Pakistan's private Geo TV.
The parishioners were attending the Sunday mass when the explosions occurred in the Qissa Khawani bazaar, one of the oldest areas in the city in the country's restive Khyber Pakhtunkhwa province..
Peshawar's commissioner Sahibzada Anees told reporters that two suicide bombers struck when the service had just ended, adding special security had been in force to protect the church.
Television footage showed ambulances rushing the wounded to hospital.
Grieved relatives gathered outside the church and shouted slogans against police over the security lapse.
"Terrorists have not spared mosques, temples and churches. Please have mercy on us," a man outside the church said.
An emergency has been declared at hospitals across the city.
Pakistani Prime Minister Nawaz Sharif strongly condemned the bombings.
"Terrorists have no religion and targeting innocent people is against the teachings of Islam and all religions," he said in a statement. (Read)
No group claimed has responsibility for the blasts, but radical Islamists have been blamed for previous attacks on the country's minority communities, including Christians.
Christians make up about four percent of Pakistan's population of 180 million and tend to keep a low profile in a country where Sunni Muslim militants frequently bomb targets they see as heretical, including Christians, Sufis and Shi'ites.