Both senior leaders had been sent back to the United States in May while the allegations were investigated and could possibly face administrative punishments.
"The commanding officer and command master chief of an East Coast-based Naval Special Warfare command were relieved of their duties on July 9," said Lt. Jacqui Maxwell, a spokesperson for Naval Special Warfare Group Two.
"Cmdr. Jarrod Donaldson and Master Chief Jon Franklin were relieved from their position by Capt. Jamie Sands, commander, Naval Special Warfare Group Two," Maxwell added.
"Donaldson and Franklin have been administratively reassigned to Naval Special Warfare Group Two.”
In early May, Donaldson and Franklin were "pulled from deployment" in East Africa after sexual misconduct allegations were made. Both leaders retained their command positions within the unit stateside while the allegations were investigated.
One of the team leaders was investigated for the alleged inappropriate touching of a female service member during the deployment, two defense officials said.
Both team leaders are being investigated for allegations of sexual harassment, officials said.
Donaldson and Franklin were investigated by a command investigation and the Navy's Criminal Investigative Service (NCIS) investigated personal conduct allegations against Franklin, Lt. Maxwell said.
They have been relieved of their duties now that the investigations are concluded. "The Navy will follow due process," Maxwell said.
Substantiated allegations are typically followed by potential nonjudicial punishments meted out by a commanding officer, a disciplinary review board or both, a defense official said. SEAL Team units deployed to East Africa typically operate in Djibouti, where the United States has a base, and in Somalia, where they assist in an advisory capacity with the Somali military.
While "pulled from deployment," both senior leaders have not been relieved of their duties as the commanding officer and command master chief of their SEAL Team. While stateside they will remain in those positions as the allegations are investigated.
The Navy has eight SEAL team units, four odd-numbered units stationed in Coronado, California, and four even-numbered units stationed at Little Creek, Virginia.
A ninth SEAL Team is more commonly known as SEAL Team Six, though its official name is Special Warfare Development Group DEVGRU. That elite Special Missions unit is best known for its role in the Osama bin Laden raid.