But the US magazine said revisions such as removing the parenthesis "Arabian Gulf" for the Persian Gulf, were common.
Iran had said in November that it was banning the new edition of the atlas, as well as National Geographic journalists, until the map for the Gulf region was changed.
It objected to the eighth edition's use of the term Arabian Gulf in parenthesis beside the more commonly used Persian Gulf.
National Geographic defended the twin terms for the Gulf.
Its website said while Persian Gulf was the primary name, "we want people searching for Arabian Gulf to be able to find what they're looking for and not to confuse it with the nearby Arabian Sea".
Changing the map
However, on 30 December, National Geographic announced it was changing its map to drop the Arabian Gulf in parenthesis.
"We review our cartographic policies on an ongoing basis"
Carol Seitz, spokeswoman for
The revised map, published on its website, bears a note in the middle of the Gulf saying that while most people call it the Persian Gulf, "this body of water is referred to by some as the Arabian Gulf".
Iran's official news agency on Monday quoted Foreign Minister Kamal Kharrazi as saying National Geographic had made a "retreat" that was "a victory for every Iranian".
In the Washington headquarters of National Geographic, spokeswoman Carol Seitz said the company had made thousands of changes to the Atlas in the five years between its seventh and eighth editions.
"We review our cartographic policies on an ongoing basis," Seitz said. The consultations leading up to the revision had involved Iranian government officials and others, she added.
Seitz denied that National Geographic had been influenced by Iran's ban on the atlas and its journalists.
Iran had also objected to the eighth edition's description of the Gulf islands of Abu Musa and Greater and Lesser Tunbs as "occupied".
Iran controls the islands, but the United Arab Emirates (UAE) claims them.
The revised map deletes the term "occupied".
Asked if National Geographic envisaged protests from the UAE over the deletion, Seitz said: "We haven't received any yet."
National Geographic's revision exists only on the internet so far.
The eighth edition was published in October. When the revision might appear in a reprint of the atlas depends on future sales and demand.