News of the measure had caused concern among secular Turks who believed it was a sign the country was becoming "too Islamic".
But Temel Kotil, the airline's chief executive has revealed the order had been made by over-zealous junior managers without consulting higher management.
He told Reuters: "As to the lipstick, we had no problems but somehow low-level managers put together a paper without asking us and that paper leaked to the media and became a big issue."
Denying the ban would come in force, he added: "We are a great global carrier and we know what we are doing."
The ban, announced a fortnight ago, promised to forbid the use of pink, red and claret colours, as well as tattoos, high buns and wigs.
Atilay Aycin, president of the airline's Hava-Is labour union, denounced it. "This new guideline is totally down to Turkish Airlines management's desire to shape the company to fit its own political and ideological stance," he said.
Turkey's Opposition Republican People's Party deputy leader Gürsel Tekin also criticised the move.
""This regulation is perversity, is there any other explanation? Does the public authority decide what a 20 or 30-year-old woman will wear," The Herald Sun quotes him as saying.
In a statement reported by The Telegraph, the airline initially defended the ban, saying: "Simple make-up, immaculate and in pastel colours, is preferred for staff working in the service sector."
The newspaper points out the airline - which is 49 per cent state owned - stopped serving alcohol in recent months.
Turkey is 99% Muslim but the Nato state and EU candidate has a secular constitution.
Turkey's Transportation and Communication minister Binali Yıldırım was evasive when asked about the ban.
Speaking at the Turkish-American Civilian Aviation Conference, Hürriyet Daily News reports his only comments on the matter as: "I think red is a beautiful colour.
"It is the same colour as the national flag's colour."