Sarraj said Field Marshal Khalifa Haftar, whose forces control much of eastern Libya, had refused to meet him on Tuesday in Cairo "without justification or reason".
The parties had missed "another precious opportunity that we hoped would be the beginning of a solution to the state of division and suffering" in Libya, he said in a statement.
"Intransigent political stances and oversized egos" were preventing a resolution to the conflict, he said.
Libya has been submerged in chaos since the fall of longtime dictator Moammar Gaddafi in 2011.
A UN-backed deal signed in Morocco in late 2015 gave birth to Sarraj's fragile unity government based in Tripoli, but gave Haftar no role in Libya's future.
The Government of National Accord has since struggled to impose its authority across the country, particularly in the east where a rival administration holds sway, backed by Haftar's forces.
The controversial head of the self-styled Libyan National Army has established himself as a key player, especially after seizing the country's key oil terminals in September.
Last week, UN envoy Martin Kobler said that negotiations on "possible amendments" to the 2015 accord had been underway for two months.
The Egyptian army hosted Sarraj and Haftar in Cairo this week for talks. They were set to meet but Sarraj said they did not meet face to face.
The army announced on Wednesday that the two sides had agreed to form "a joint committee" to come up with amendments to the deal that set up the unity government.
But Sarraj said the talks had "failed".
Haftar's rivals accuse him of wanting to establish a military dictatorship in Libya.
The foreign ministry in Tunis said on Wednesday that the chief diplomats of Tunisia, Algeria and Egypt would meet on March 1 in the Tunisian capital to discuss the Libyan crisis.