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The earthquake, the second to hit the region in less than 12 hours, occurred at 7.07 am and the location was 64 km east of Siliguri, it said.
The depth was 10 km, it added.
There was no immediate report of any damage or losses, officials said.
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The impact was also felt in parts of Sikkim.
On Monday night, an earthquake of 5.4 magnitude hit Sikkim with tremors being also felt in the states of Assam, West Bengal and Bihar.
The quake occurred at 8.49 pm at a depth of 10 km near the India-Bhutan border.