The Red Crescent in the worst-hit province of Nangarhar said 12 people were killed there, while one person was confirmed dead in neighbouring Kunar province.
"The number of dead is expected to rise as the search operation is still ongoing," said Nangarhar Red Crescent chief Nagyalay Yusufzai.
He said more than 60 people were hurt in the quake, which sent people rushing from their homes and was felt in the Afghan capital Kabul and in Islamabad in neighbouring Pakistan.
The quake, measured at a magnitude of 5.6 by the US Geological Survey, struck at 0925 GMT at a depth of 62 kilometres.
Its epicentre was 24 kilometres northwest of the Nangarhar provincial capital Jalalabad, near the Pakistani border, the USGS said.
Nangarhar government spokesman Ahmad Zia Abdulzai gave a different figure of nine confirmed dead in his province and said more than 100 were injured.
"There has been widespread damage in some affected villages since most of the houses there are mud-built," he told AFP.
One person was killed and one injured in Kunar and many homes were destroyed, said its spokesman Wasefullah Wasef.
In Kama district outside Jalalabad, people ran from their homes in panic when the tremor was felt, a witness said, describing it as "very powerful".
In a separate natural disaster, flash floods Tuesday in the northern province of Balkh killed at least 11 people and left three missing, said Munir Ahmad Farhad, a provincial government spokesman.
"The floods have also damaged close to a thousand homes as well as hundreds of hectares of farmland," the spokesman said Wednesday.
"The badly affected areas are impoverished villages where most of the homes are mud-built and can be easily damaged when floods come. We are worried as it is raining again now."
Afghanistan is frequently hit by earthquakes, especially in the Hindu Kush mountain range which lies near the juncture of the Eurasian and Indian tectonic plates.
In June 2012 two quakes in the area triggered landslides that killed at least 75 villagers.
Wednesday's tremors came a week after a 7.8-magnitude earthquake centred in Iran affected thousands of people in remote southeastern Pakistan and killed 41 people.
Pakistani victims have staged angry protests, accusing the government of failing to provide adequate relief after hundreds of homes were destroyed or damaged.
COMMENTS (13)
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These frequent recent Earthquakes in the Region are Earthquake Swams. They could be signs of a major earthquake in near future. According to work done by Dr Roger Bilham: Kashmir Gap slip potential in the region may be in the range 9-14m, which would be associated with an earthquake as large as Mw=8.9.
Only NGO doing serious work on earthquake awareness and mitigation is FOCUS Humanitarian Assistance Pakistan. NDMA should learn from their community based approach to disaster mitigation
@Salman:
"Day of Judgment is approaching. May Allah have mercy on us."
Every year when there's flood or earthquake you say the same.
in Gilgit-Baltistan too
@Salman: Seems like day of judgement is only approaching in our area as rest of the world is not experiencing any earth quakes.
It was a 5.7 magnitude earthquake. Although your Web Desk managed to take a screen shot from the USGS website, it did not bother to update the relevant numbers. Please correct. Reference: http://earthquake.usgs.gov/earthquakes/eventpage/usb000geu9#summary
what iran and afghanistan doing these days?
Oh Allah. Have mercy on Pakistan..!
Something is fishy now - too many earthquakes in this region all of a sudden!
it feels like above 7 and half here in islamabad
It was very huge. Reminded me of 2008 earthquake