The three victims, whose nationalities have not been disclosed, were found in the northern and eastern side of the island.
The initial tremor in the north of the island was followed by two strong secondary quakes and more than 100 aftershocks.
"We jumped out of our beds to avoid anything falling on our heads", said Jean-Paul Volckaert who runs a hotel near Senggigi on the western side of Lombok. "There was about 20 seconds of shaking, the water in the pool was making quite large waves".
At least 162 people were injured, including 67 hospitalized with serious injuries, Nugroho said.
A magnitude 6.5 quake struck off the north-east Coast of Sumatra Island in 2016, killing dozens of people and displacing more than 40,000.
The quake struck at 6.47 am local time (5.17 am Indian Standard Time), and its epicentre was located 50 km northeast of Mataram city on Lombok, The Guardian reported.
The initial quake struck at 7 a.m. local time (8 p.m. Saturday U.S. ET), and was followed by 60 smaller earthquakes with the largest one recorded at 5.7 magnitude.
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Injury, and also has to go back'. "Antonio Valencia comes from holiday, I think too much holiday for him". "You can not imagine how much I have enjoyed these two weeks with these guys".
Hiking at Mount Rinjani had been suspended due to landslides but the Bali airport was operating normally, the U.S. Embassy in Jakarta tweeted.
As authorities sought to assess the damage to buildings and infrastructure on Lombok, popular trekking trails on the remote Mount Rinjani were closed because of landslides, according to the disaster agency.
Television footage showed residents remaining outside, fearing aftershocks, as the injured were being treated on mattresses taken out of their houses and patients were wheeled out of a hospital.
A shallow magnitude 6.4 natural disaster has hit Lombok killing 10 and injuring 12.
No tsunami alert has been issued.
In December 2004, a massive 9.1-magnitude natural disaster off Sumatra triggered a tsunami that killed 230,000 people in a dozen countries.
Lombok is the next island east of Bali.
Indonesia is prone to earthquakes because it lies on the Ring of Fire - the line of frequent quakes and volcanic eruptions that circles virtually the entire Pacific rim.