"The strike is ongoing until our demands are met," an official at the transport ministry said, declining to be named because he was not authorized to speak publicly to media.
Officials at Sanaa, Aden and Mukalla airports confirmed the shutdown.
Chaos hit the Sanaa and Aden airports with stranded passengers asked to return home, witnesses said.
"Some passengers protested and tried to storm the airport," one witness at Sanaa airport said.
The aviation authority falls under the supervision of the transport ministry.
The dispute started when the finance ministry decided to appoint a financial official at the authority, which says its finances are independent.
The freezing of the aviation authority's funds has prevented it from paying workers' wages and other operating costs, a statement by the authority's workers union said.
SHI/SHI