Another US official confirmed to CNN that the remains were bone fragments.
The remains were recovered on November 12 by a US military and FBI team that traveled to the area. Johnson's family was notified on Monday the official said.
"On Nov. 12, 2017, a joint US Africa Command military investigation team discovered additional human remains at the site where Sgt. La David T. Johnson's body was recovered following the Oct. 4 attack," a statement released by Pentagon spokesperson Dana White on Tuesday said.
"Today, we can confirm that the Armed Forces Medical Examiner has positively identified these remains as those of Sgt. Johnson."
There has been no public disclosure about whether these additional remains will provide any clues about Johnson's death or what happened to his body during the 48 hours he was missing.
US officials are also investigating local eyewitness reports Sgt. Johnson was found with his hands tied, a defense official told CNN earlier this month, though the US military has not confirmed those accounts.
A joint US Africa Command and Niger military investigation team returned to Tongo Tongo, the village near where the attack took place on October 4.
According to US Africa Command, investigators interviewed local villagers, physically examined multiple areas of interest and retraced actions before, during and after the ambush.
What happened to Johnson and how he became separated from the rest of the Green Beret-led team after it was attacked is one of the key mysteries surrounding the incident.
Johnson was reportedly found nearly a mile away from the central scene of the ambush in Niger that killed him and three other US soldiers.
and The Washington Post
have reported eyewitnesses of the aftermath disclosing his hands were tied.
The Post quoted a local farmer and trader saying some children tending cattle found Johnson's remains with his hands tied behind his back and talked to a village chief confirming it.
Authorities, according to the official, are also investigating whether local villagers may have taken his body at some point before it was turned over to Nigerien forces.
Johnson's body was recovered in a remote area of the northwestern African country by Nigerien troops nearly 48 hours after he was discovered to be missing in the wake of the attack, according to US officials.
Several US military officials caution the local reports are not yet verified.
The Green Beret-led team was traveling with 30 Nigerien soldiers when they were attacked by approximately 50 ISIS-affiliated fighters armed with rocket propelled grenades, mortars and heavy machine guns. The team became separated during the firefight, US officials and a Nigerien soldier told CNN.
During the subsequent gun battle, which lasted for hours, four US soldiers were killed and two were wounded. Five Nigeriens were also killed. US-Nigerien forces managed to kill 20 militants during the firefight according to a defense official.
The Defense Department has said it expects the investigation into the Niger ambush to be completed by January.
"The Department of Defense is committed to a thorough and detailed investigation into the deaths of Staff Sgt. Bryan C. Black, Staff Sgt. Jeremiah W. Johnson, Staff Sgt. Dustin M. Wright and Sgt. La David T. Johnson. Once the investigation is completed, briefing the families of the fallen will be the Department's first priority," a statement released last month said.