In a statement issued by U.S. Central Command, officials say one U.S. service member is missing and five others aboard the craft have been rescued after the crash, which took place about 20 miles (32 km) off the southern coast of Yemen at 7 p.m. (16000 GMT).
A U.S. official told Reuters that the cause of the crash was under investigation.
"When the incident took place the helicopter was not very high above the water," CENTCOM spokesman Colonel John Thomas said.
The United States has been carrying out air strikes against al Qaeda in Yemen, with at least 80 launched since the end of February.
A small number of ground raids using U.S. Special Operations forces have also taken place, including one in January which resulted in the death of a U.S. Navy Seal.
There have been a number of aviation mishaps involving U.S military aircraft in the past few months.
The U.S. Coast Guard recently said that it had suspended its search off Hawaii for five Army aviators missing since their Black Hawk helicopter crashed earlier this month.
In April, a Black Hawk U.S. Army helicopter crashed on a Maryland golf course, killing one crew member and seriously injuring two others.
Last month, a military transport plane crash killing 16 service members including elite special operations forces in northern Mississippi.