Two Libyan army units used heavy artillery in an exchange of fire overnight centring on a barracks in a densely populated area of southeast Tripoli, the military command said.
An attack early Friday saw members of a security group set up by ex-premier Fayez al-Sarraj target Al-Tekbali barracks, the headquarters of 444 Brigade, Tripoli military commander Abdelbaset Marouane said on Facebook.
The elite 444 Brigade posted on Facebook that one of its officers, Second Lieutenant Omrane Belgassem, was killed.
Brigadier General Marouane said in a video message that the security group attacked the barracks after midnight on his orders after 444 Brigade "ceased to obey military orders".
The noise of heavy artillery in action was heard throughout the city from just after midnight and lasted until early on Friday morning.
Columns of smoke still hung in the air near the barracks after the fighting stopped, a resident of the heavily populated Salaheddine area in the suburbs told AFP by phone.
Presidential council chief and supreme army commander Mohamed al-Manfi ordered "all forces which have clashed or are still clashing in Tripoli to immediately cease fire and return to their barracks without delay".
Also using Facebook, he threatened those who fail to obey his orders with criminal prosecution and warned: "Further such incidents will no longer be tolerated."
The United Nations Support Mission in Libya (UNSMIL) in a statement expressed its "grave concern" about the clashes and urged all parties to "exercise maximum restraint".
UNSMIL also called on "all relevant authorities to assume their responsibilities in ensuring the protection of civilians and in exercising control over their respective units".
"UNSMIL reminds all parties of their obligations under international humanitarian law to ensure the protection of civilians and civilian infrastructure," the statement said.
The incident was a reminder of the precarious security situation in the North African country nearly a decade after the overthrow of dictator Moamer Kadhafi.
Repeated outbreaks of fighting ended with a UN-backed ceasefire last year.
That paved the way for peace talks and the formation of a transitional government this March, ahead of elections set for December.
But preparations are marred by disputes between key stakeholders over when to hold elections, what elections to hold, and on what constitutional grounds.
