The Obama administration is facing criticism for sending mixed messages about the tense situation in Yemen.

Pentagon sources confirmed to Fox News that the USS Theodore Roosevelt is tracking the Iranian convoy, and also launching F/A-18 Hornets to conduct "manned reconnaissance" of the estimated nine Iranian ships.

Those ships are suspected of carrying weapons to rebel fighters in Yemen.

State Department spokeswoman Marie Harf denied Tuesday that the U.S. ships' presence has anything to do with Iran's support of the Houthi rebels in Yemen.

She called out "misreporting," saying the ships are there to make sure shipping lanes remained open and safe. 

Earlier today on "Fox and Friends," White House communications director Jen Psaki refused to say exactly why the U.S. ships were sent. 

Steve Doocy pointed out statements by senior Pentagon officials, who said the U.S. forces were there to intercept Iran's ships. 

"I'm not going to lay out what actions may or may not be taken. That would be irresponsible from here," said Psaki, adding that the administration wants a de-escalation of the situation and to move toward a "diplomatic solution" to the Yemen crisis.

Bill Hemmer discussed all of this with Fox News strategic analyst Lt. Col. Ralph Peters, who said President Obama does not want to do anything to jeopardize an agreement with Iran on its nuclear program.

Peters said right now he believes there are internal disagreements among those in the Obama administration as the president pursues the nuclear agreement with Iran.

"Basically you've got an amazing split, with the Pentagon saying we've got to support our traditional allies, which happen to be Sunni in the Middle East. And the Kerry State Department and the administration doing everything it can to appease Iran. [They're] chasing this nuke deal, this unicorn notion that we can have a grand reconciliation with Iran. You've got basically the Pentagon trying to hold together the old alliances and the administration just abandoning them," said Peters. 

He noted reports that the administration pressured its close ally, Saudi Arabia, to stop its airstrikes on the Houthis in Yemen. 

The Saudis announced Tuesday they would halt the bombing campaign amid a worsening humanitarian crisis in Yemen.

"The administration doesn't want to do anything to alienate Iran and in fact, it's now to the point where it's doing Iran's bidding, which is one of the most preposterous situations in the history of American foreign policy," he said.

Watch his full analysis above.

UPDATE: "Happening Now" reported that the Saudi airstrikes had resumed today against the Houthis in Yemen.

Watch Jennifer Griffin's report from the Pentagon below.