Senior US officials said yesterday they had received assurances from Tehran that the crews -- take to Farsi island -- would be allowed to sail onwards come first light.
But it appeared likely that the embarrassing crisis would last at least until after President Barack Obama's State of the Union address.
Secretary of State John Kerry called his Iranian counterpart Foreign Minister Mohammad Javad Zarif, with whom he struck the Iran nuclear deal.
Washington has no diplomatic relations with Tehran, but Kerry and Zarif forged a tie during the long negotiations for the pact and are in regular contact.
"We have been in touch with the Iranians. We have been assured of their safety and that they will be able to move forward on their journey promptly," she said.
"Obviously, any situation like this we take very seriously, and that's why we acted very quickly to get in touch and determine as much as we can."
A US defense official, speaking on condition of anonymity, said one or both of the vessels -- small patrol boats -- may have had a "mechanical incident."
The tiny territory extends Iranian waters deep into one of the world's most important shipping lanes, an oil superhighway and potential military flashpoint.
"Earlier today, we lost contact with two small US naval craft en route from Kuwait to Bahrain," a senior US administration official said.
American officials did not dispute that the vessels appeared to have been in Iranian territorial waters when they were intercepted by Tehran's forces.
"At this early stage," another senior administration official said, there is "nothing to indicate that" Iran had committed a hostile act.
Obama is expected to use his much-heralded final State of the Union address to burnish his legacy, hailing, among other things, the nuclear deal with Iran.
The deal foresees the Islamic republic scaling back its nuclear program to put a bomb outside its immediate reach in exchange for relief from international sanctions.
The deal is to be implemented very soon -- Kerry has said "in the coming days" -- but has been criticized by Obama's US opponents as too soft on Tehran.
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