The attacks by suspected Islamist militants in Lahore city targeted the Ahmadi sect, which has experienced years of state-sanctioned discrimination and occasional attacks by radical Sunnis. It has never before been hit on such a large scale or coordinated fashion.
One of the attackers climbed atop the minaret of one of the mosques, firing an assault rifle and throwing hand grenades, TV footage showed. Outside, police were engaged in a fierce gunfight with the attackers, an Associated Press reporter at the scene said.
Police officer Imtiaz Ahmad said several attackers were inside and were suspected to be holding hostages.
Outside the other mosque several kilometers (miles) away, a witness complained of police inaction when the attackers struck.
"I asked the policeman to open fire. He told me he could not because he only had four bullets in his gun," said Ghalib Hussain.
Dr Rizan Nasir said 20 people had been killed in one mosque. Figures were not available for the other.
Pakistan has seen scores of attacks by groups of Islamist militants against government, Western and security force targets over the past three years. Lahore, the second largest city in the country and a vital a military and political center, has been the scene of several.
Many Islamist militants believe it is permissible or honorable to kill non-Muslims, or even those Muslims who do not share their views.
The Ahmadis call themselves Muslims but believe their founder declared himself a prophet centuries after Muhammad, who other Muslims believe was the final prophet. They have long been subject to informal and state-sanctioned discrimination in Pakistan.
An Ahmadi spokesman said the sect abhors violence and was deeply concerned about the attacks.
"We are a peaceful people and monitoring the situation and hoping and praying that the authorities are able to take all necessary action to bring the situation to normalcy with the least number of casualties," Waseem Sayed said via e-mail from the United States, where he lives.
Under pressure from hard-liners, the Pakistani government in the 1970s declared the Ahmadi a non-Muslim minority. They are prohibited from calling themselves Muslims or engaging in Muslim practices such as reciting Islamic prayers.
There are an estimated 4 million Ahmadis in Pakistan out of a total Muslim population of around 170 million.
