The U.S. military launched cruise missile strikes on Thursday to knock out three coastal radar sites in areas of Yemen controlled by Iran-aligned Houthi forces, retaliating after failed missile attacks this week on a U.S. Navy destroyer, U.S. officials said.

The strikes, authorized by President Barack Obama, represent Washington's first direct military action against suspected Houthi-controlled targets in Yemen's conflict.

Still, the Pentagon appeared to stress 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.

U.S. officials, speaking on condition of anonymity, said U.S. Navy destroyer USS Nitze launched the Tomahawk cruise missiles around 4 a.m. (0100 GMT).

"These radars were active during previous attacks and attempted attacks on ships in the Red Sea," including the USS Mason, one of the officials said, adding the targeted radar sites were in remote areas where the risk of civilian casualties was low.

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

Shipping sources told Reuters sites were hit in the Dhubab district of Taiz province, a remote area overlooking the Bab al-Mandab Straight known for fishing and smuggling.

The failed missile attacks on the USS Mason appeared to be part of the reaction to an air-strike that killed 140 mourners at a funeral attended by powerful tribal leaders in Yemen's Houthi-held capital Sanaa.

The Houthis, who are battling the internationally-recognized government of Yemen President Abd Rabbu Mansour al-Hadi, denied any involvement in Sunday's attempt to strike the USS Mason.

On Thursday, the Houthis reiterated a denial that they carried out the strikes and said they did not come from areas under their control, a news agency controlled by the group reported 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 Sunday's attempted strikes, in which two coastal cruise missiles designed to target ships failed to reach the destroyer.

Yemen is of crucial importance for the U.S., as the country is home to one of their worst enemies, al-Qaida's deadliest franchise, al-Qaeda in the Arabian Peninsula (AQAP), which has orchestrated numerous high-profile terrorist attacks, including claiming responsibility for the Charlie Hebdo massacre in Paris. Since 2002, the U.S. has been conducting counterterror strikes and operations against radical militants as part of U.S. national security policy. The U.S's "targeted-killing policy" and practices by the Obama administration have raised serious laws-of-war concerns regarding the human cost of U.S security policy in Yemen.