Christians in Lahore responded to the attacks by holding a rally
Schools run by Christian missions in Pakistan's Karachi city have closed for three days to mourn the killings of Christians in Punjab province.
Schools and colleges across Pakistan are closed for summer vacations, but vacations in Karachi ended on Monday.
At least six Christians were killed in religious unrest in Punjab during the weekend, after days of tension sparked by the rumoured desecration of a Koran.
Officials said the rumours which led to the unrest were false.
Saturday's attack happened in a neighbourhood in Gojra town in Punjab when six Christians were burnt to death and scores of houses were set on fire by a Muslim mob.
The attack followed allegations that members of the Christian community had desecrated a Koran, the Muslim holy book.
Southern Karachi city is home to some of the best known mission schools and colleges in the country.
They decided not to open for three days in protest over the Gojra killings when summer vacations ended on Monday.
The Associated Press news agency quoted Sadiq Daniel, Bishop of the Diocese of Karachi and Balochistan, as saying that the Christians wanted to register their anger and concern peacefully.
The government "must bring all perpetrators of the crime to justice," he said.
Attacks against minority religious groups in Muslim-majority Pakistan have been common and have often gone unpunished, says the BBC's M Ilyas Khan in Islamabad.
On Sunday, following protests by the Christian community, the police charged hundreds of people, including two top police officials, for perpetrating the attack.
A spokesman for Pakistan's president said a judicial panel would probe the incident.