Witnesses said a few women and children fainted due to suffocation at the end of congregation when a gate of the seminary run by Dawat-e-Islami was opened and the women started rushing outside.
City police chief Niaz Siddiqui told AFP the stampede was triggered when a girl fell while the women were leaving the mosque.
Witnesses said the child cried out, sparking panic among the women who tried to force their way out of the mosque.
Twenty-two bodies were placed in Liaquat National Hospital while seven more bodies were brought to Jinnah Hospital. Police said around 100 people were injured.
Siddiqui said seven of the 19 women admitted to hospital are in critical condition.
The victims were mostly aged women, said Dr Seemi Jamal at Jinnah Hospital. Several women were unconscious, she added.
"I saw a large number of women coming out of a small gate just after the annual women's congregation ended," said Mohammad Altaf, brother of an injured woman. "Several women were crushed by the crowd coming out of the hall."
"All of a sudden there had been screams and shouts. Everyone ran for safety and we too," Haleema Bibi, one of the participants told Reuters. "We were just shouting. We did not know what has happened." "Women fell on each other as panic spread. It was an absolute mayhem. Nobody knew what has happened," another woman said.
Asif Ejaz Sheikh, district police officer, said there was no indication the incident was a terrorist act. "Initially, it was said that a phone call was received by the mosque organisers that a bomb was planted in the mosque. But we have checked and there was no phone call. It was just a rumour," he said.
Thousands of pairs of shoes were seen littered outside the mosque. Relatives wailed and beat their chests as ambulances ferried dead and injured people to hospitals. "My mother has died. My mother has died," a boy named Nasir shouted and fainted as he identified his 55-year-old mother, Rabia Bibi, among the dead at Liaquat Hospital.
Hospital staff made announcements through megaphones, urging people to donate blood.
CONDOLENCES: President General Pervez Musharraf and Prime Minister Shaukat Aziz on Sunday expressed deep sorrow and grief over the tragic loss of life at Faizan-e-Madina mosque, Karachi. They also expressed solidarity with bereaved families. The president and Prime Minister talked to Sindh governor Dr Ishratul Ibad and chief minister Dr Arbab Ghulam Rahim and inquired about the incident.
They instructed provincial authorities to provide all medical care and support to the injured and affected families. They prayed the departed souls may rest in peace and may Allah Almighty grant their family members the courage and strength to bear the loss.
Sindh governor Dr Ishratul Ibad Khan, expressing grief on the Sunday's tragic incident here at Faizan-e-Madina, has announced financial support of Rs100,000 each for the families who lost their beloved ones and Rs30,000 each for the injured.
In a condolence message here, the governor prayed to the eternal peace of the departed souls and quick recovery of the injured, He also prayed for grant of strength to the bereaved families to bear the irreparable loss with fortitude.
He directed concerned officials to take every possible step for effective medical treatment of the injured. Sindh Chief Minister Dr Arbab Ghulam Rahim has expressed profound grief and sorrow over the loss of precious lives in the stampede.
Dr Arbab has also issued directives for conducting an inquiry into the incident besides ensuring provision of every possible facility for the treatment of the injured.
City Nazim Syed Mustafa Kamal has also expressed deep sorrow and grief on the death of women and children in the incident. After receiving the sad news, Kamal talked to central leader of Dawat-e-Islami Yaqoob Attari on the telephone from Malaysia to express his condolences besides assuring full co-operation of the City Government, said a statement here on Sunday.
He directed the DCO Karachi to reach the site of the incident while emergency was declared in all the hospitals of the City Government.
Fire tenders and rescue teams also rushed to the scene on the directive of the City Nazim.
He ordered for provision of every possible medical treatment to the injured and warned that no negligence in this regard would be tolerated. The DCO Karachi and Chief Fire Officer quickly reached at the site and called all the concerned officials.
CDGK has set up a camp at Faizan-e-Madina where information regarding victims could be obtained, besides other support. Special teams are engaged in providing medical facilities to the injured and other relief work.
City Nazim has cut short his visit of Malaysia and would be coming back to Karachi by Monday. He is continuously in touch with the officials concerned and members of Dawat-e-Islami.
Acting City Nazim Nasreen Jalil also expressed sorrow and rushed to the hospitals on the getting the sad news. Talking to the media, Nasreen Jalil said all expenses on the medical treatment of injured would be born by the city government. She also prayed for Eisal-e-Sawab of departed souls and expeditious recovery of the injured.