McMahon said it was too early in the investigation to identify suspects or possible motives, but he vowed to use whatever resources necessary to "bring these suspects to justice."
"It's too early to tell if its [drug] cartel-related or any other suspects," he said. "But, again, the investigation is early and we have not had an opportunity to read all their reports."
Joseph McStay's brother, Mike McStay, told reporters that the confirmation of the identities of his two relatives afforded some amount of peace for the family.
McMahon said autopsies were planned to obtain the rest of the identities.
"We have no idea how long they've been there," he said.
The family went missing in February 2010. When family and friends had not heard from them for several days, Mike McStay, called authorities.
"The bottom line," the lead investigator in the case, Troy Dugal, told The Times in 2011, "was that life was normal for the McStays up to Feb. 4, and on that day they just vanished."
At the time, Joseph was 40 and Summer was a 43-year-old stay-at-home mom, described as fiercely protective of her boys, Gianni and Joseph Jr.
Investigators found out that the family's SUV had been towed from the parking lot of a strip mall in San Ysidro, an hour's drive from the McStays' Fallbrook home and a short walk from a pedestrian crossing into Mexico.
Investigators examined surveillance footage from the border crossing, and among the thousands who crossed the border that day investigators saw a man holding the hand of a young boy followed by a woman holding the hand of another boy.