Adamos Aspris, spokesman for airport operator Hermes, said six departures and six arrivals will be affected by the strike, which will run from 7:00 pm to 8:00 am on Sunday (1700-0600 GMT).
Controllers in Paphos and the country's main airport in Larnaca walked out on Friday and have also declared for strike action on March 7, 12 and 15.
The controllers' union said they were escalating action after talks with the government had broken down, with their proposals having been "dismissed without being examined" and there being "no willingness for a dialogue."
The controllers are seeking exemption from a two-year public sector pay freeze, and also have grievances over manning levels, overtime and paying pension contributions.