A group of anti-American demonstrators attacked three US sailors whose warship, the missile-guided destroyer USS Ross, docked in Istanbul yesterday.
"We define you as murderers, as killers… and we want you to get out of our land," one of the demonstrators in the video said.
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The sailors fled to their ship without being injured.
After the video was circulated online, the Turkish Foreign Ministry released a statement condemning the attack, the New York Times said.
"[It is a] disrespectful act, which is in no way tolerable", a Turkish Foreign Ministry spokesman said.
The US embassy in Turkey labelled the attack "appalling".
"While we respect the right to peaceful protest and freedom of expression, we condemn today's attack in Istanbul, and have no doubt the vast majority of Turks would join us in rejecting an action that so disrespects Turkey's reputation for hospitality", the Embassy tweeted.
Colonel Steve Warren, a Pentagon spokesman, promised to work with the Turkish authority to investigate the incident, the Washington Post reports.
Turkey is a member of the NATO and has long been a key US ally in the Middle East, but according to Reuters "anti-American sentiment runs deep in parts of society, particularly since the 2003 U.S.-led invasion of Iraq".