The tremor of 6.7 magnitude struck the mountainous Hindu Kush region bordering Pakistan early on Tuesday, it said.
Residents in Pakistan-administered Kashmir, where tens of thousands died in October’s earthquake, fled their homes.
The tremor was also felt in India’s capital, Delhi. There were no immediate reports of casualties.
More than 73,000 people were killed in the earthquake which left at least three million people homeless, according to officials in Pakistan.