Mexico's organised crime groups often abandon multiple bodies in public places as warnings to their rivals, and authorities said at least a few of the recent victims had tattoos of the Santa Muerte cult popular among drug traffickers.
But Nuevo Leon state Attorney General Adrian de la Garza said he did not rule out the possibility that the victims were US-bound migrants.
The bodies of the 43 men and six women were found in the town of San Juan on the non-toll highway to the border city of Reynosa at about 4 am (1430 IST), forcing police and troops to close off the highway.
Nuevo Leon state security spokesman Jorge Domene said at a news conference that a banner left at the site bore a message with the Zetas drug cartel taking responsibility for the massacre.
Domene said the fact the bodies were found with the heads, hands and feet cut off will make identification difficult. The bodies were being taken to Monterrey for DNA tests.
De la Garza said the victims could have been killed as long as two days ago at another location, then transported to San Juan, a town in Cadereyta municipality, about 175 kilometres west-southwest of McAllen, Texas, or 125 kilometres southwest of the Roma, Texas, border crossing.