It also reported a 5.4-magnitude quake at 2.21am on Tuesday, close to the site of Sunday's 6.9-magnitude quake.
The governor of the province that includes Lombok, the military and the national search and rescue agency issued different death tolls that ranged from 226 to 381.
'We still need long-term aid, even though we have already received help from various (regional) governments, ' national disaster agency spokesman Sutopo Purwo Nugroho said.
Tens of thousands of homes, businesses and mosques were levelled by the quake, which struck on Sunday.
The aftershock comes after Sunday's devastating 6.9-magnitude quake, which relief agencies said had wiped out entire villages in the worst-hit regions of northern and western Lombok.
The footage of the prayer led by Imam Arafat at the Musholla As-Syuhada Mosque was being broadcast live on Facebook on Sunday night when a magnitude 7.0 quake hit the neighboring Lombok Island.
Relief efforts had yet to reach parts of the island even before Thursday's aftershock, Indonesian authorities said, with hopes fading of finding further survivors among the wreckage.
A Reuters witness said the latest quake sent people into the streets in panic and caused buildings to collapse.
Most people live in basic housing in small communities.
He estimated 75 per cent of houses are damaged in some villages in east and north Lombok.
Aid groups say children are particularly vulnerable, with many sleeping in open fields and suffering illnesses from lack of warm clothing and blankets. There are growing concerns that the important tourism industry will be badly hit at what should be a busy time.
Thousands of tourists have left Lombok since Sunday, fearing further earthquakes, some on extra flights provided by airlines and others on ferries to the neighbouring island of Bali.
"We've lost a lot of bookings and future guests are in wait-and-see mode".
Indonesia's geological agency said the quake on Thursday afternoon had a magnitude of 6.2 and was shallow, at a depth of 12 kilometres, centred in the north-west of the island.
Indonesia is prone to earthquakes because of its location on the "Ring of Fire", an arc of volcanoes and fault lines in the Pacific Basin.