Authorities are now clearing the school "room by room", the Daily Times reported.
The two victims were students at the school police said, adding that no other injuries were reorted. Officials say parents will be reunited with their children at McGee Park in nearby Farmington, New Mexico.
Though the shooting at Aztec High School was confirmed by the San Juan County Sheriff's Office, there are still conflicting number of casualties.More news: Valve's Portal Series Returns In Bridge Constructor Portal
Other schools in the area also were locked down as a precaution.
The city of Aztec is located in the northwest corner of New Mexico and has a population of almost 7,000 people. That was confirmed shortly after by San Juan County Sheriff Ken Christesen. He did not say whether anyone had been injured or killed.
Per the statement, the school will be placed on lockdown for roughly "three to four hours".