A school, student hostel and the home of a priest were also torched in the incident near the town of Sangla Hill, about 80 miles northeast of the major eastern city of Lahore, said area police official Ali Asghar Dogar.
The attacks came a day after a local Muslim resident accused Yousaf Masih, a Christian, of burning a one-room Islamic school along with copies of the Quran.
Dogar said no one was injured in the attacks, which were being investigated. About two dozen people had been arrested over the incident, he said.
Protesters also burned tires on village roads and blocked traffic for several hours.
Shahbaz Bhatti, head of the All Pakistan Minorities Alliance, which promotes the rights of minorities in mainly Sunni Muslim Pakistan, denied the charges and condemned the attacks.
"No Christian burned copies of the Quran," he told The Associated Press. "No Christian even can think of doing it," he said. "We have maximum regard and respect for the Quran and Islam's Prophet Muhammad."
Local Muslim leaders used mosque public address systems to urge Muslims to attack the churches, Bhatti said.
Dogar said police were also investigating the burning Friday night of the Quran school.
"Some people told us last night that it was done by Yousaf Masih, and we have registered a case against him," Dogar said. Another police official, Pervez Rahim, said Masih had been detained as part of the investigation.
However, Dogar said the allegations against Masih were apparently leveled by people who lost money while gambling with him on Friday.
"We don't know who is right and who is wrong, but the fact remains that hundreds of people today attacked two churches and burned them," he said, adding that the situation was "now under control."
Pakistan is an Islamic country where non-Muslims comprise just 3 percent of the 150 million-plus population. The country's Christian minority generally coexists peacefully with the Muslim majority, although there have been occasional attacks on churches and Christian clergy by Islamic extremists railing against Western influence in Pakistan.
Thousands of Pakistanis joined angry street protests this spring over the alleged desecration of the Quran by interrogators at a U.S. military prison in Guantanamo, Bay, Cuba.