The population has dramatically dropped despite the arrival of navy reinforcements in the upper Gulf of California in April 2015 to enforce a ban on fishing gillnets blamed for the vaquita's death.
The porpoise's population had already fallen to fewer than 100 in 2014, down from 200 in 2012, according to the International Committee for the Recovery of the Vaquita (CIRVA), a global group of scientists.
Mexico's environment ministry said in a statement that a joint study with CIRVA between September and December estimated the latest population at "around 60."
The vaquita's fate has been linked to another critically endangered sea creature, the totoaba, a fish that has been illegally caught for its swim bladder, which is dried and sold on the black market in China.
Also Read
Poachers use illegal gillnets to catch the totoaba and the vaquita, a shy 1.5-metre-long (five-foot) cetacean with dark rings are the eyes, is believed to be the victims of bycatch.
President Enrique Pena Nieto imposed a two-year ban on gillnets in April 2015 and increased the vaquita protection area tenfold to 13,000 square kilometres.
Environment Minister Rafael Pacchiano said three vaquitas had been found dead and that protective measures needed to be reinforced, but federal authorities are convinced that the vaquita can still be saved.
He urged the local population to report illegal activities.
The Mexican government agreed to compensate local fishermen in a USD 30 million a year program to give up gillnet fishing while they look for safer alternative nets.
But navy sailors told AFP during a tour of their mission last month that they were catching gillnets every day -- three to 10 times the length of a football field, often ensnaring totoabas, dolphins, turtles and sea lions.
Officials say fishermen sell the totoaba's swim bladders to smugglers who store them in border towns before sending them to the United States or shipping them directly to Asia in suitcases or through parcel services.