The CH-53 helicopters went down around 5.30pm local time on Friday in the waters near Ras Siyuan in northern Djibouti, a US military statement said.
"There were a total of 12 crew members aboard at the time of the crash," the statement said. "Djiboutian military members near the impact site responded immediately and were able to rescue two injured crew members," it said
The Marine Corps helicopters were on a night training mission near Godoria Range, it said.
There was no reason to believe hostile fire was involved in the crash, CNN said, quoting US officials
The two rescued crew members were listed in stable condition after being flown to Camp Lemonier, the main base in Djibouti of the US military's Joint Task Force Horn of Africa, the statement said.
"The status of the remaining crew members is uknown at this time," the statement said. A search was underway by Djiboutian, US and French forces, it said.
About 1700 US troops are based in Djibouti as part of a joint task force that conducts training and exercises with other militaries in the region.