The grey men’s top features a red map of the Chinese mainland but fails to include territories including Taiwan.
Furious shoppers posted images of the t-shirt on Chinese social media network Weibo.
They pointed out that the map didn't include the self-ruled island that Beijing regards as Chinese territory.
The map also appeared to leave out southern Tibet and the disputed South China Sea, the state-owned Global Times said.
The photos were taken at a Gap shop in Canada's Niagara region, Global Times said.
The company “sincerely apologised for the unintentional error” and insisted it respected China’s “sovereignty and territorial integrity".
The garment has been pulled from shelves, a statement added.
Bosses vowed to implement “rigorous reviews” in the wake of the error.
China noted Gap's apology and "will follow carefully their actions and remarks later on," Foreign Ministry spokesman Lu Kang told reporters in Beijing.
Gap is the latest in a string of companies forced to apologise for perceived slights to China's sovereignty.
Delta Air Lines, hotel operator Marriott and fashion brand Zara are among businesses to say sorry to China for referring to Taiwan, Hong Kong, and Tibet as countries.
