The government has allocated $3 million for the plan, to be matched by funds from international conservation groups.
The environment ministry said the "ambitious emergency plan" to save the vaquita marina porpoise would be carried out with help from international conservation groups.
However, the plan is controversial with conservationists, some of whom say the vaquita is not an animal that can thrive in captivity.
Scientists warned in February that there are only 30 vaquita remaining, saying the species faced extinction by 2022.
The porpoise is native to the Gulf of California, where illegal fishing nets are threatening to wipe it out.
Under the Mexican plan, "some animals will be transferred to a refuge, where they will be able to reproduce without the risk of being caught in gillnets," the environment ministry said.
"However, experts recognize that there is uncertainty about how the porpoises will behave during the search, capture and temporary relocation to the refuge."
The government has allocated $3 million for the plan, to be matched by funds from international conservation groups, it said.
The most common cause of death for the vaquita is getting caught in illegal gillnets meant to catch another endangered species, a large fish called the totoaba.
In China, dried totoaba swim bladders are considered a delicacy and can fetch $20,000 per kilogram.