Responding to complaints by Israel's Tourism Ministry, the U.S. State Department revised a travel advisory issued five days ago.
The State Department's advisory came just after a terror cell fired five Grad-type rockets at the southern Israeli resort city of Eilat.
Two of the missiles landed in the Red Sea, one hit an empty field just north of the hotel strip in Eilat, and two others exploded in front of the Intercontinental Hotel in the nearby Jordanian port city of Aqaba, killing a Jordanian cab driver and wounding three passersby.
The State Department's travel advisory warned Americans visiting Eilat and other cities in southern Israel to note the location of bomb shelters. The advisory did not mention Aqaba, where the fatality and injuries occurred.
Israeli Tourism Minister Stas Misezhnikov responded without delay.
"This advisory gives a prize to terror and undermines regional stability and the sense of security that Israel gives to everyone who enters the country," Misezhnikov said in a statement.
"Differentiating Israel from its neighbor, which actually suffered loss of life, is improper and lacks balance," he said.
State Department spokesman P.J. Crowley said travel advisories were "based on our best judgment of the assessment of risk wherever American citizens are traveling. So I would say that it's not our judgment that the risk is identical between the two locations."
Despite Crowley's assessment, the State Department revised the warning.
The new advisory simply says Americans visiting southern Israel "should be aware of the risks and should follow the advice of the government of Israel's office of Home Front Command," without singling out Eilat.
AP contributed to this report.