The ministry said 1,117 people had been injured in Tuesday's 7.3-magnitude quake which hit in remote mountain districts northeast of Nepal.
The US Geological Survey said Tuesday's quake hit in the early afternoon in an isolated, conservation area between the capital of Kathmandu and Mount Everest.
Tuesday's quake was felt as far away as New Delhi, and officials said it caused buildings to collapse in Tibet in neighbouring China.
Tuesday's quake hit at a depth of 15km, according to the USGS, and was followed by a series of lesser aftershocks measuring from magnitude 5.6 to 6.3.
The tremors in Kathmandu lasted close to a minute according to an AFP correspondent in the city, with the ground swaying. Sirens could be heard soon afterwards although there were no immediate reports of casualties.
People were seen running screaming onto the streets of Kathmandu and nearby cities, while telephone connections were down.
"Looks like Nepal will be destroyed completely this time," one resident shouted, while others were putting up tents in open spaces that they had only recently taken down.
Three aftershocks were felt in the following minutes, as shops started shutting and people tried to stock up on food.
An earlier report by the European-Mediterranean Seismological Centre put the magnitude at 7.1.
The tremor was felt over the border in the neighbouring Indian state of Bihar, as well as in Delhi.
Quake-prone Nepal is located where the Indian tectonic plate runs into, and under, the Eurasian plate.
Relief teams from around the world are still working to provide water, food and medical assistance to Nepalis following the April 25 quake.
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