Indonesia's health ministry has said it fears thousands of people may have died.
Rick Cameron, the director of Island Aid, a disaster relief organisation in Indonesia, said he had been taken by surprise by the second tremor.
He told Al Jazeera: "We all jumped up, ran to a grassy area outside the house. As we went down the stairs it intensified. Some of my friends fell over, it was so strong.
"It was extremely disorienting and shakes every perspective of what you think the world is."
It was unclear how many injuries the second earthquake had caused, but Raphael Abreu, a geophysicist with the US Geological Survey, told Al Jazeera that it had been "definitely capable of creating, by itself, significant damage to structures and property".
Step Vaessen, Al Jazeera's correspondent reporting from Padang, said: "So far, the worst incident I've seen is 160 people buried at one location.
"It's sporadic damage, but the damage is serious. High-rise buildings, many of which have collapsed totally or partially - so lots of people trapped ... but it is still hard to say how many have died.
"I haven't seen many rescue workers active at all. I don't think there's enough equipment at the moment in Padang to conduct these operations."
The UN said the death told had risen to 1,100 - up from 770 given by the disaster ministry. About 290 people were badly injured while 2,090 were slightly injured.
Fauzi Bahar, Padang's mayor, appealed for help on Indonesian radio saying the city was "overwhelmed".
"We really need help. We call on people to come to Padang to evacuate bodies and help the injured," he said.
Susilo Bambang Yudhoyono, Indonesia's president, instructed officials to "flood" Padang with aid and medical relief, while his government announced $10m in emergency aid.
He has been to Padang to oversee the relief effort and "gave a little message, asking people to pray for a miracle to help the city", said Al Jazeera's Veronica Pedrosa.
Vaessen reported that medical teams and military aircraft had been arriving with field hospitals, tents, medicine and food rations as officials ramped up the rescue and relief operation.
At daybreak on Thursday, many Padang residents used their bare hands to dig through the rubble searching for survivors.
Survivors were seen being pulled out and hospitals struggled to treat the many injured.
Officials in Padang said about 500 houses had caved in and witnesses said many buildings had collapsed after the first earthquake.
Priyadi Kardono, a spokesman for Indonesia's disaster management agency, said the effects "could be as big as the Yogyakarta quake", referring to a 2006 disaster that killed or injured more than 5,000 people and damaged or destroyed 150,000 homes.
The tremor was felt in the Indonesian capital Jakarta, 940km away, and sent frightened office workers streaming out of buildings in Singapore as well as Malaysia's capital, Kuala Lumpur.
Dozens of aftershocks followed.
'Ring of Fire'
Padang, the capital of Indonesia's West Sumatra province, sits on one of the world's most active fault lines along the so-called Ring of Fire, the same one that cracked off Aceh, at the northern tip of Sumatra, in 2004 to trigger the Indian Ocean tsunami.
|Shopping malls, hospitals and hotels in Padang were among the structures toppled [Reuters]
That disaster killed more than 220,000 people in Indonesia, Thailand, Sri Lanka and India among other countries.
Padang was badly hit by an 8.4 magnitude quake in September 2007, when dozens of people died and several large buildings collapsed.
Scientists had been warning of a major earthquake in the area for a long time, but the Indonesian government has said it did not have funds for disaster-preparation measures, our correspondent said.
Geologists warn the low-lying city and surrounding area could be vulnerable to more seismic activity.
"There are three big volcanoes in west Sumatra - Merapi, Talang and Tandikat," Surono, the head of the Geological Disaster Mitigation and Volcanology Centre in Indonesia, said.
"We fear that this quake might cause volcanic eruptions there."