The company said they would be undertaking "rigorous reviews" to ensure that it doesn't happen again.
Lee also reiterated the government's stance on the matter, asking the airline not to belittle Taiwan or damage its sovereignty and dignity by bowing to pressure from China.
One user on the Chinese social network Weibo complained the retailer may have intentionally left out Taiwan and other islands claimed by Beijing in the South China Sea.
The Gap map also did not reflect Chinese claims to territory in the northeastern Indian state of Arunachal Pradesh, which China refers to as "Southern Tibet", or show its claims in the South China Sea, which overlap with those of several other countries in the region.
Gap is not the first global brand to bruise China's long fingers and tender toes, but it has apologized just the same.
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The Global Times quoted Gap as saying that the T-shirt had not been released in China.
"Upon the realization that one of our T-shirts sold in some overseas markets mistakenly failed to reflect the correct map of China, we urgently launched an internal investigation across the group and have made a decision to immediately pull back this T-shirt from all the concerned global markets", Gap said in a statement. "The related products were pulled off the shelves in the Chinese market and destroyed earlier".
USA hotel chain Marriott, Spanish clothing giant Zara and a slew of airlines have faced China's wrath for not classifying Taiwan as part of China on their websites.
The White House in early May called Chinese demands, that over 30 worldwide airlines including a few in the US, remove from their websites any data that might suggest that Hong Kong, Macau and Taiwan were not part of China, as being Orwellian nonsense.
The statement continued by saying the company sincerely apologizes for the unintentional error and an internal inspection is being conduct because of the discovery.