The quake struck at around 2:52 am and was situated at a depth of 10 kilometres, the IMD said.
The quake, which had its epicentre in the Andaman islands, occurred at 6:09 am, the National Centre for Seismology said.
According to the Japan Meteorological Agency (JMA), the quake occurred at 2:34 am (local time) and occurred at a depth of 30 km.
The strong quake struck at a depth of 37 kilometres in the far west of the country near the Costa Rican border, according to the US Geological Survey.
Japan sits at the junction of four tectonic plates and experiences a number of relatively violent quakes every year.
The tremors were felt at 4.32 am and the epicentre of the earthquake was at a depth of 10 kilometre in northeast of Mandi, Shimla Meteorological Centre Director Manmohan Singh.
The government must ensure seismic safety, scientists from all over the country who gathered here last week for a global workshop said.
The quake comes one after another quake that hit near Manila a day before.
Scientists from the US Geological Survey logged its magnitude at 6.3, and said its epicentre was 40 kilometres (25 miles) below the Earth's surface.
Local media said the quake had been felt all over the island and a highway connecting Yilan and Hualien was shut down due to falling rocks.
The Beijing Earthquake Agency has organised experts to analyse the seismic event, the state-run Xinhua news agency reported.
The news agency also reports that Captain Cook resident Elizabeth Cano said on Facebook that her whole house shook in the quake.
The quake hit off the coast of eastern Sulawesi, on the other side of the island from disaster-hit Palu, where residents still felt the tremor despite being hundreds of kilometres away.
There were no reports of any casualties, injuries or damage to property. No tsunami warning has been issued.
The agency says the earthquake struck a spot 26 miles (42 kilometers) southwest of Aiaktalik island at 7 p.m. Saturday.