By Phil Stewart

WASHINGTON (Reuters) - The U.S. military launched cruise missiles on Thursday against three coastal radar sites in areas of Yemen controlled by Iran-aligned Houthi forces, after failed missile attacks this week on a U.S. Navy destroyer, U.S. officials said.

Yemen's Houthi movement condemned the strikes and Iran announced it had sent two warships to the Gulf of Aden, according to the semi-official Tasnim news agency, establishing a military presence in waters off Yemen.

The U.S. missile strikes, authorized by President Barack Obama, represent Washington's first direct military action against suspected Houthi-controlled targets in Yemen's conflict and raised questions about the potential for further escalation.

The Pentagon, however, stressed the limited nature of the strikes, aimed at radar that enabled the launch of at least three missiles against the U.S. Navy ship USS Mason on Sunday and Wednesday.

"These limited self-defense strikes were conducted to protect our personnel, our ships and our freedom of navigation," Pentagon spokesman Peter Cook said.

In a news conference later, Cook said the strikes were not connected to the broader civil war in Yemen, which has unleashed famine and killed more than 10,000 people since March 2015 in the Arab world's poorest country.

The U.S. military said U.S. Navy destroyer USS Nitze launched the Tomahawk cruise missiles around 4 a.m. (0100 GMT) at radar sites located in remote areas where the risk of civilian casualties was low.

One U.S. official identified the areas in Yemen where the radar were located as near Ras Isa, north of Mukha and near Khoka.

The Houthi movement, which has denied being responsible for the missile attacks on the Mason, warned that it too would defend itself.

"The direct American attack targeting Yemeni soil this morning is not acceptable," Brigadier General Sharaf Luqman, a spokesman for Yemeni forces fighting alongside the Houthis, was quoted as saying by the Houthi-controlled Saba news agency.

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Iran, which supports the Houthi group, said it had deployed two warships to the Gulf of Aden, to protect ship lanes from piracy. An Iranian official told Reuters the vessels were deployed a few days ago, but declined to say when they will arrive.

BACKLASH OVER SUSPECTED SAUDI STRIKE

The failed missile attacks on the USS Mason appeared to be part of the reaction to a suspected Saudi-led strike on mourners gathered in Yemen's Houthi-held capital Sanaa last week.

The Houthis, who are battling the internationally-recognized government of Yemen President Abd Rabbu Mansour al-Hadi, denied the missiles were fired from areas under their control, a news agency controlled by the group quoted a military source as saying.

The allegations were false pretexts to "escalate aggression and cover up crimes committed against the Yemeni people," the source said.

U.S. officials have told Reuters there were growing indications that Houthi fighters, or forces aligned with them, were responsible for the attempted strikes, in which coastal cruise missiles designed to target ships failed to reach the destroyer.

Senator John McCain, the chairman of the Senate Armed Services Committee, said the missiles fired at the USS Mason were likely provided by Iran.

The missile incidents, along with an Oct. 1 strike on a vessel from the United Arab Emirates, add to questions about safety of passage for military ships around the Bab al-Mandab Strait, one of the world's busiest shipping routes.

The Houthis, who are allied to Hadi's predecessor Ali Abdullah Saleh, have the support of many army units and control most of the north, including the capital Sanaa.

The Pentagon warned against any future attacks.

"The United States will respond to any further threat to our ships and commercial traffic, as appropriate," Cook said.

The United Arab Emirates (UAE), a leading member of a Saudi-led Arab coalition fighting to end Houthi control, denounced the attacks on the Mason as an attempt to target the freedom of navigation and to inflame the regional situation.

Michael Knights, an expert on Yemen's conflict at the Washington Institute for Near East Policy, suggested the Houthis, fighters from a Shi'ite sect, could be becoming more militarily aligned with groups such as Lebanon's Shi'ite militant group Hezbollah.

"Targeting U.S. warships is a sign that the Houthis have decided to join the axis of resistance that currently includes Lebanese Hezbollah, Hamas and Iran," Knight said.

(Additional reporting by Mohammed Ghobari in Sanaa, Katie Paul in Riyadh and Parisa Hafezi in Istanbul, Editing by William Maclean, Ralph Boulton and Chris Reese)