Mexican Attorney General Marisela Morales said authorities have found 116 bodies near the border.
The death toll is 28 more than previously reported, Morales said Tuesday.
Suspects with ties to the Zetas drug gang have been linked to the killings.
Morales said 17 people, who purportedly confessed to abducting passengers from buses in the northern state of Tamaulipas and killing them, have been taken into custody.
President Felipe Calderón said a 19-year-old man who is among the detained confessed to killing more than 200 people. Calderón gave no other details.
Interior Secretary Francisco Blake Mora pledged to step up the presence of troops and federal police in the area where the killings occurred and not leave the area until the killers and drug gang members there have been caught.
"Organized crime, in its desperation, resorts to committing atrocities that we can't and shouldn't tolerate as a government and as a society," Blake said.
The graves were found earlier this month in the township of San Fernando, the same area of Tamaulipas where investigators found the bodies of 72 migrants massacred by suspected drug cartel gunmen last August. Most of the 72 migrants were Central Americans, who frequently travel through the area to reach the United States.
Police say witnesses in the latest killing case have told them that gunmen pulled the victims, mostly young men, off passenger buses traveling through the San Fernando area in late March. Authorities blame the abductions on the Zetas drug gang, the same group accused in the migrant killings.
The motive for the bus abductions remains unclear, though prosecutors have suggested the gang may have been forcefully recruiting people to work for it.
San Fernando is a town about 90 miles (145 kilometers) south of Brownsville, Texas, on a well-traveled stretch of highway that runs near the Gulf Coast. It is an area regularly patrolled by the Mexican military.
The Zetas and rival Gulf Cartel are fighting in Tamaulipas over lucrative drug transit routes to the U.S.
Authorities are working to identify the bodies, one of which may belong to a U.S. citizen, through DNA samples and other techniques.
One of the bodies is a Guatemalan man, the government of that Central American nation said.
The victim has been identified as Feliciano Tagual Ovalle, 44, the Guatemalan Foreign Ministry said in a statement late Monday. The statement did not say whether the man was a migrant passing through or a resident of Mexico.
It said the Guatemalan government planned to bring the body home.
Mexican authorities confirmed one victim was Guatemalan and said another was a man from central Mexico. Mexican prosecutors had previously said most of the bodies were probably Mexican citizens.
Based on reporting by The Associated Press.