Xinhua said the city of Guangyuan, north of the provincial capital Chengdu, was particularly hard hit with about 71,300 homes being destroyed and more than 200,000 in danger of collapsing, an earthquake relief official in the city of Guangyuan, told Xinhua.
The aftershock is the strongest to have hit Sichuan province since the devastating quake of May 12.
The death toll from the initial tremor has exceeded 62,500 and aid is still being delivered to the disaster zone.
Conditions for millions of survivors living in makeshift camps worsened as rain fell throughout the day and forecasters predict heavy downpours overnight.
Sunday's aftershock measured 6.4 on the Richter scale, an official with the Sichuan Earthquake Bureau told the AFP news agency, making it the strongest since the level eight quake that destroyed large swathes of Sichuan.
The US Geological Survey put the magnitude of Sunday's aftershock at 5.8.
The aftershock compounded fears of further destruction stemming from the May 12 disaster, the worst earthquake in China in more than 30 years.
The government said the quake left 69 dams in danger of bursting and had created "dangerous situations" at hundreds of others.
E Jingping, the vice minister of water resources, said in Beijing that authorities had taken steps to alleviate the danger by draining and lowering the water levels at hundreds of reservoirs.
The death toll from the initial quake has continued to rise.
On Sunday the government said 62,664 people were killed by the quake and 23,775 remain missing.
More than 5.4 million people have been left homeless.
Wen Jiabao, China's prime minister, said on Saturday that the final toll could climb higher than 80,000 as he toured quake-hit Sichuan province with Ban Ki-moon, the UN secretary-general.
The prime minister said the government needs 900,000 tents for the survivors and has urged Chinese manufacturers to make 30,000 a day.
Relief teams were working around the clock to set up temporary housing and provide food and medical care to the displaced.
A Russian military transport plane, one of 12 that are expected, carrying tents, blankets, field hospitals and other supplies landed in Chengdu, state media reported.
A French medical team has also arrived in Chengdu and had left for Guangyuan.
Although state media reported that an 80-year-old man was pulled from the rubble on Friday, rescue teams say the search for survivors is over, and the focus is now on clean-up and reconstruction operations.
Saad Attia, a member of a Dutch aid team in the town of Hanwang, told AFP: "I think we have a lot of work to do today, but it will be only finding dead bodies. I don't think there are any more survivors."
Ban Ki-moon, the UN secretary-general, arrived from neighbouring Myanmar on Saturday and praised China's response to the earthquake.