Protesters in a neighborhood of Karachi, the country's largest city, faced off with police and security personnel who used teargas to disperse the crowd, witnesses said.
All missionary schools and colleges in Karachi were closed for three days of mourning, GEO TV News reported.
Two suicide attacks at the All Saints Church in Peshawar killed 81 people and injured more than 140 Sunday.
After the attacks, relatives of the victims and other members of the Christian community placed bodies on a highway, blocking traffic.
Relatives of the victims broke windows of the Lady Reading Hospital to protest the absence of medical personnel and a shortage of beds and medicine, Dawn News reported. The relatives charged that many of the injured died because of the absence and negligence of doctors.
Prime Minister Nawaz Sharif and other political leaders condemned the bombings.
Chief Minister of Khyber Pakhtunkhwa Pervez Khattak called the bombings a conspiracy against the government.
Qaumi Watan Party chairman Aftab Ahmad Khan Sherpao called them a brutal act against humanity.
Awami National Party representative Mian Iftikhar Hussain blamed the attacks on the government's inability to come up with strategies to restore peace and counter terrorism.
About 600 worshipers had gathered at All Saint's Church, where many members of the congregation were participating in a food giveaway on the front lawn when the bombs exploded.
The Pakistan Ulema Council, the nation's largest clerical body, issued a statement saying the group was "standing with our Christian brothers in this tragedy."