"There was a navigational error of some kind," Carter said. He stopped short of blaming the 10 young sailors in the crew.
The incident occurred Tuesday, just hours before President Barack Obama gave his final State of the Union address and set off a flurry of high-level diplomatic activity to gain the release of the boats and the sailors on Wednesday.
Carter was careful not to assign initial blame to the sailors, their equipment or their commanders for possibly giving the crews the wrong navigation plan until the Navy can complete an investigation, which was already underway. However, he said the sailors "were clearly out of the position they intended to be in."
Carter made the remarks at the headquarters of U.S. Central Command in Tampa, Florida, where he introduced Army Gen. Joseph Votel, the head of Special Operations Command, as his choice to replace Army Gen. Lloyd Austin as Centcom commander.
"He was my only recommendation to the president to succeed Lloyd," the secretary said of Votel.
Austin, who will be retiring, said he was leaving to Votel a campaign that was making progress against the Islamic State of Iraq and Syria, or ISIS, also known as ISIL. "We are in fact doing what we set out to do," he said.
Iran's seizure of the two 49-foot Riverine Command Boats, and the jarring videos on Iranian media of U.S. sailors made to kneel on deck in custody, dominated the brief question-and-answer period that followed the introductions of Austin and Votel.
Carter skirted a question on the video showing one of the U.S. sailors apologizing for straying into Iranian waters. White House Press Secretary Josh Earnest said Obama has seen the videos and "he's obviously interested in learning more about the situation."
"I don't like to see our people being detained by a foreign military," Carter said, but "we don't know the full context. We need to give these guys the opportunities to tell us what was really going on before we can know. I want to give them the chance to describe what happened."
The videos also showed the Iranian Revolutionary Guards confiscating the weapons aboard the two patrol craft and lining them up on deck. Austin interjected that "the gear that they deployed with was largely there when we got the boats back," but the Navy was conducting an inventory.
Debriefings of the sailors have already begun, Carter said.
"The information that they have given us, and through their commanders, is that they did stray accidentally into Iranian waters due to a navigation error," he said earlier in an interview with FUSION television's Jorge Ramos which was airing on Spanish-language Univision.
The Navy and the Pentagon have said that the two boats were en route from Kuwait to Bahrain, headquarters of the Navy's Fifth Fleet, when they were intercepted by Iranian Revolutionary Guard Corps vessels.
The most direct route likely would have kept the two boats close to the western coastline of the Persian Gulf but the two boats were seized within the three-mile territorial limit of Iran's heavily-guarded Farsi Island in the middle of the Gulf.
It was unclear whether engine trouble aboard one of the boats may have contributed to the navigation error.
"They did not report this navigational error at the time" to commanders, Carter said. "It may be that they were trying to sort it out at the time they encountered the Iranian boats and discovered they were inside of the territorial waters of Iran."
Carter also dismissed speculation that the two boats may have been on a covert mission to scope out the island. "They were simply transiting from one place to another," he said.
-- Richard Sisk can be reached at Richard.Sisk@Military.com.