The officials spoke on condition of anonymity because they were not authorized to discuss the ship movement on the record.
The Houthis are battling government-backed fighters in an effort to take control of the country. The U.S. has been providing logistical and intelligence support to Saudi Arabia-led coalition launching airstrikes against the Houthis. That air campaign is now in its fourth week.
The U.S. Navy generally conducts consensual boardings of ships when needed, including to combat piracy around Africa and the region. So far, however, U.S. naval personnel have not boarded any Iranian vessels since the Yemen conflict began.
Army Colonel Steve Warren, a Pentagon spokesman, denied to Reuters that the ships were on a mission to intercept Iranian arms shipments to Yemen.
White House spokesman Josh Earnest would not comment specifically on any Navy movements in Yemeni waters, but said the U.S. has concerns about Iran's support for the Houthis.
"We have seen evidence that the Iranians are supplying weapons and other armed support to the Houthis in Yemen. That support will only contribute to greater violence in that country. These are exactly the kind of destabilizing activities that we have in mind when we raise concerns about Iran's destabilizing activities in the Middle East."
He said "the Iranians are acutely aware of our concerns for their continued support of the Houthis by sending them large shipments of weapons."