The program can also be used by victims, expert witnesses, police and judges who are in danger because of their role in a legal proceeding.
The president's office says in a decree published Friday that the plan will go into effect within six months.
Mexico currently has a much more limited program which provides limited protection to cooperating witnesses in federal cases.
But the new plan could give such witnesses new identities in different cities, to avoid reprisals.
The program may help in prosecuting violent drug cartels whose turf battles have cost Mexico more than 47,500 lives over the last 5 1/2 years.