The mass grave found in Veracruz state could be the largest in Mexico, state attorney general Jorge Winckler told CNN affiliate Televisa.
Veracruz is "one big mass grave," Winckler told the affiliate Tuesday.
The remains appear to be victims of organized crime violence killed in recent years.
The identification process has been slow and complicated, Winckler said, but authorities are working to match the skulls using information on the database of missing people.
He did not say when the mass grave was discovered, but some of the skulls were found with the help of members of Colectivo Solecito, a group of mothers and other relatives of the missing.
For more than two years, the group has searched for their loved ones at the Colinas de Santa Fe area, near the Veracruz harbor.
Martha González, who's part of the group, said she will finally get closure.
"They give us just the bones, but at least I can have them, I can keep it some place where it won't be rained on, where I can put a flower on it," she told CNN en Español.
"And I can know that they are really there and resting."
Her son, a police officer, disappeared with five colleagues in 2013.
'There's peace in my heart'
Authorities have identified the remains of Pedro Alberto Huesca, an official from the state attorney general's office. He disappeared four years ago after helping dismantle a local cell of the Zetas cartel.
His mother, Griselda Huesca, said after years of uncertainty, she can finally be at peace.
"I am so sad to have found him like that, but there's peace in my heart because he was found, and didn't end up left there like a dog," she told CNN en Español.
"He's where he needs to be, with his family, and not in that hole they threw him in."
Groups such as Solecito have a lot of work to do.
Government data show between January 2014 and January this year, at least 722 people vanished in Veracruz.
Victims of drug cartels
The state on Mexico's Gulf Coast has long been a playground for drug cartels, with raging turf wars among gang members.
Drug cartels have been behind the disappearances of people in the region, according to Winckler. The mass grave could have been their makeshift cemetery.
In recent years, mass graves containing apparent victims of organized crime have made headlines in Veracruz, including 11 bodies found near a tourist area this month.
Bodies dumped on roads
In 2012, the dismembered bodies of four people, including three journalists, were found in a canal in the state. The victims appeared to have been tortured, authorities said at the time.
A year before that,
dozens of bodies were found dumped on a roadway and other locations throughout the state.
The government said this month that it will send federal police to help fight violence in Veracruz.