The airport said that in the past three weeks, two drivers made their way along the taxiway and across a runway.
The app had directed users to drive along the taxiway, but did not tell them to go onto the runway.
A temporary fix has now been issued that tells anyone searching for directions that they are "not available" instead of showing the earlier route.
The airport said it contacted Apple three weeks ago via the local attorney general's office.
"We asked them to disable the map for Fairbanks until they could correct it, thinking it would be better to have nothing show up than to take the chance that one more person would do this," said Melissa Osborn, chief of operations at the Alaskan airport.
She added that barricades have been erected to block access to the taxiway and that they will only be removed when Apple updates its directions.
The first instance of a driver making it onto the runway was an out-of-state visitor trying to return a rental car before a flight and the second was an Alaska resident trying to get to the airport. Both vehicles were safely escorted away when airport personnel saw them.
Both drivers said they were following directions on their iPhones.