Members of the Third Force militia loyal to the UN-backed Government of National Accord in Tripoli attacked an airbase used by military strongman Khalifa Haftar's self-proclaimed Libyan National Army, military sources said.
There was no independent word on casualties in the assault on the Brak al-Shati base, but Libyan media reported at least 60 dead.
"I am outraged by reports of significant numbers of fatalities, including civilians and by reports that summary executions may have taken place," UN envoy Martin Kobler said in a statement.
The unity government, the rival administration in eastern Libya and their respective backers are battling for influence in the North African country which has been wracked by chaos since the fall of dictator Moammar Gaddafi in 2011.
The LNA does not recognise the authority of the GNA and instead supports the rival authorities based in the east.
Britain's ambassador to Libya, Peter Millett, also denounced the airbase assault.
"Disgusted by attack on Brak al-Shati amp;amp; reports of mass executions. Perpetrators must be brought to justice," he wrote on Twitter.
The incident at the Brak base in Wadi al-Shati district comes a month after an attack by the LNA on the Tamenhant airbase controlled by the Third Force near the region's main city of Sebha further south.
That attack was abandoned after a reconciliation meeting between Haftar and unity government head Fayez al-Sarraj in Abu Dhabi on May 2.
The speaker of the eastern-based parliament, which is supported by the LNA, accused the Misrata-based Third Force of a "serious breach of the truce agreement reached in Abu Dhabi".
Aguila Saleh said there were a "number of martyrs" in LNA ranks, without giving a figure.