The regional seismological centre in Shillong told PTI that the quake measured 5.5 on the Richter scale and took place around 1.25 am.
The quake was also felt in Itanagar, Guwahati and Agartala, besides Nagaland, the sources said.
The tremor epicentre was latitude 25.5 degrees north and longitude 94.2 degrees east in Kohima area of Nagaland.
It originated 35 km below the surface, India Meteorological Department sources said in Kohima.
Today's quake follows the one on July 1 which measured 5.4 on the Richter scale and its epicentre was located in Phek region of Nagaland.
Official sources said there was no report of any casualty or damage to property either in Meghalaya or Nagaland.