"There have been -- there are, obviously -- flights coming from Iran. Every single week there are flights from Iran and we've traced it and know this," Kerry told PBS television in an interview.
"Iran needs to recognize that the United States is not going to stand by while the region is destabilized or while people engage in overt warfare across lines, international boundaries in other countries."
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The Huthis have seized control of large parts of Yemen, including the capital Sanaa, and joined forces with security forces who have remained loyal to longtime strongman Ali Abdullah Saleh, forced from power in 2012 after a year-long, Arab Spring-inspired uprising.
Riyadh accuses Tehran, the major Shiite power, of backing the Huthis. But Iranian Foreign Minister Mohammed Javad Zarif insisted his government wanted a swift end to the fighting, which has cost more than 640 lives since March 19, according to the World Health Organisation.
Kerry said Washington was not looking for confrontation with Tehran.
"But we're not going to step away from our alliances and our friendships and the need to stand with those who feel threatened as a consequence of the choices that Iran might be making."
It was Kerry's first television interview since his return to Washington after negotiating a framework agreement with Iran last week reining in its controversial nuclear program.
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