The Navy said it responded Thursday to a distress signal from the Indian-flagged vessel Premdivya which said it was fired upon by men in a skiff who were trying to board their vessel.
In a statement from the 5th Fleet's Bahrain headquarters, the Navy said a helicopter from the USS Vella Gulf fired two warning shots at the suspected pirates to stop them fleeing. U.S. forces searched the skiff and found weapons including rocket-propelled grenades, then took nine suspected pirates aboard the American ship.
Officials were gathering evidence on the incident and may hand the suspects to Kenyan authorities for prosecution, Pentagon spokesman Bryan Whitman said. The United States agreed last month to hand pirate suspects to the east African nation.
On Wednesday, the same American ship detained seven other suspected pirates - the Navy's first arrests since it established an anti-piracy task force this year.
Those suspects, armed with AK-47s and rocket-propelled grenades, had tried to board the Marshall Islands-flagged vessel Polaris using a ladder from their skiff.
The seven were transferred via helicopter to the USNS Lewis and Clark on Thursday. They will eventually be handed to Kenya, according to Lt. Nathan Christensen, a spokesman for the 5th Fleet. Associated Press Television News footage showed some of the men, handcuffed and wearing leg shackles and white jumpsuits, being escorted from helicopters onto the ship.
They were given a meal, a blanket, a towel and a bar of soap, but they were not allowed to talk to each other. U.S. forces assisted by a translator were trying to get information from the men, such as their ages and nationalities.
The men were then taken to a holding area surrounded by razor wire where they were watched by U.S. forces.
Pirates, mostly from lawless Somalia, have become an increasing problem in the region. Last year, pirates seeking multimillion-dollar ransoms attacked 111 ships in the Gulf of Aden and seized 42 of them, including the Ukrainian ship, the MV Faina.
That vessel docked at Mombasa on Thursday. The ship's captain had died of a suspected heart attack during the kidnapping.
"It is very difficult to express our feelings because the voyage is too hard for everybody," the acting captain, Viktor Nikolsky, said in broken English during brief comments to journalists at the docks.
The 20 Russian and Ukrainian crew members were then whisked away for medical checks, and were expected to be flown back to Ukraine on Saturday.
The Ukrainian ship's capture sparked a diplomatic spat; while Kenya had said the weapons belonged to Nairobi, a Kenyan maritime official and several foreign diplomats said the weapons were destined for southern Sudan.
The allegations embarrassed Kenya, which had helped broker a peace deal between northern Sudan's government and the oil-rich south in 2005, ending a 21-year civil war.
Officials repeated Thursday that the tanks had been bound for Kenya.
"We have nothing to hide," Kenyan government spokesman Alfred Mutua told the banks of TV cameras assembled at the docks.
MV Faina's ordeal began in September, when scores of heavily armed Somali pirates swarmed onboard as it carried 33 Soviet-designed tanks and crates of small arms headed to Kenya. Foreign governments had feared the Faina's weapons might fall into the hands of Somali insurgents who the U.S. State Department says are linked to al-Qaida.
In an effort to stop the pirates and protect commercial shipping, warships from a number of countries including the United States, India, Britain, China, Russia, Saudi Arabia and South Korea have sent ships to the area.
Somalia has not had a functioning government since warlords overthrew dictator Mohamed Siad Barre in 1991, then turning on each other and reducing the Horn of Africa nation to anarchy and chaos.
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Associated Press reporters Barbara Surk in Dubai, United Arab Emirates, Pauline Jelinek in Washington, and Katharine Houreld in Mombasa, Kenya contributed to this report.