The map, which briefly features on the screens of a control room at a spy base in two episodes of the six-part show, depicts China's unilaterally declared "nine-dash line" and is displayed within the context of maritime claims in the region.
"Netflix's violations angered and hurt the feelings of the entire people of Vietnam," the Authority of Broadcasting and Electronic Information said in a statement on its website.
"This is the third time in a row in the last 12 months that Netflix has been found to distribute movies and TV shows containing content which violate Vietnam's sovereignty," said the statement, which was dated July 1.
The "nine-dash line" is a U-shaped feature used on Chinese maps to illustrate its disputed claims over vast expanses of the resource-rich South China Sea, including large swathes of what Vietnam regards as its continental shelf, where it has awarded oil concessions.
Chinese and Vietnamese ships have in recent years been embroiled in months-long standoffs in the disputed waterways.
Netflix confirmed it had removed the show in Vietnam but said it remained available on the service in the rest of the world.
"Following a written legal demand from the Vietnamese regulator, we have removed the licensed series, Pine Gap, from Netflix in Vietnam, to comply with local law," a Netflix spokesperson said.
In October 2019, Vietnam pulled DreamWorks' animated film "Abominable" from cinemas over a scene featuring a similar map showing the "nine-dash line".
Vietnam's broadcasting authority said the other two shows which it had raised as issues with Netflix were "Put Your Head on My Shoulder", a 2019 Chinese rom-com, and the U.S. political drama "Madam Secretary".
"Put Your Head on My Shoulder" was still visible on Netflix on Friday, although "Madam Secretary" was not.
