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The Mayor said residents are "on edge", after the other two quakes this month killed nearly 400 people.
Damage in Ixtaltepec, Oaxaca, after another earthquake earlier this month
An aftershock with a magnitude of 6.1 has hit Mexico, just days after a devastating tremor left 295 people dead.
The US Geological Survey said it was centred about 11 miles (18km) south-southeast of Matias Romero in the southern state of Oaxaca.
Mexico's National Seismological Service recorded thousands of aftershocks just in the first in the first nine and a half hours of Saturday, some of which were 4.0 or greater.
Details on damage or injuries are not immediately clear, but Mexico City Mayor Miguel Mancera said residents were already on edge since last week's quake.
:: Why are there so many earthquakes in Mexico?
A building in Mexico City flattened by another earthquake this week
Buildings swayed and a seismic alarm was set off on Saturday in the capital, Mexico City, where rescuers have been trying to reach people who remain buried in rubble from Thursday's quake.
Those rescuers have been forced to suspend their efforts.
"I heard the alarm and ran downstairs with my family," said Sergio Cedillo, a resident who was watching rescue efforts when the alarm sounded.
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Member of a specialised rescue team search for survivors in Juchitan de Zaragoza
Alejandra Castellanos, who was staying in a hotel in the area with her husband, said she was "frightened" when she felt the earth shake for the second time in two weeks.
"I was frightened because I thought: not again," she said.
Southern Mexico was hit on 7 September by a huge magnitude of 8.1 tremor.
The total death toll from the first two earthquakes is thought to be over 400.
:: The forgotten quake victims outside Mexico City
The Ring of Fire, along which 90% of the world's earthquakes occur
The Central American country suffers so much because of its position on a large grid of tectonic plates, on which all the Earth's countries and seas sit.
It also falls on the 'Ring of Fire', a horseshoe shaped area around the edges of the Pacific Ocean, from Australia to the Andes, along which 90% of all earthquakes occur.
(SKY NEWS)
