The airline's chief executive officer Temel Kotil announced the move in the Turkish media, accusing overzealous lower-level airline executives of having imposed the ban.
Video courtesy of jn1.tv
"Staff can use the color they want. This measure was not approved by the hierarchy," Kotilo said, according to Hurriyet and Milliyet newspapers.
Earlier this month, the airline defended the ban, saying in a statement that "simple make-up, immaculate and in pastel colors, is preferred for staff working in the service sector."
In recent months the booming airline – 49% state-owned – has also stopped serving alcohol on internal flights.
Numerous women had posted pictures of themselves wearing bright red lipstick on social media websites to protest at the measure.
The liberal media had accused the airline of seeking to Islamize the company under the influence of the conservative government.
Prime Minister Recep Tayyip Erdogan's Islamist-rooted Justice and Development Party, in power for over a decade, is often accused of creeping efforts to coerce the country to be more conservative and pious.
Turkey is a fiercely secular state, despite being a majority Muslim country. Under Erdogan's rule, headscarves – banned in public institutions – have become more visible in public places and alcohol bans are more widespread.