His comments come a day after the two countries hailed the implementation of Tehran's nuclear deal, with President Barack Obama saying the breakthrough was vindication of his contentious policy of engagement with Iran.
However, underlining the lingering deep suspicions between the two sides, Iran seized 10 sailors last week in the Gulf after their boats strayed into Iranian waters and held them overnight. They were freed on Wednesday after Iran accepted they entered by mistake.
Video footage showed the US Navy personnel kneeling with their hands behind their heads as they were apprehended, something Kerry made clear he was deeply unhappy about.
"I was very angry, I was very frustrated and angry that that was released," Kerry told CNN, saying the footage was released by the Iranian military or Revolutionary Guards, not the government.
"But I am not excusing it, there was no excuse for it. Our sailors regretably, and inadvertently, went into Iranian waters."
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The strongly worded remarks came as the US military released its first detailed account of the incident, which threatened to spark a renewed crisis between Tehran and Washington.
One of the two US riverine patrol boats (RCBs) "had indications of a mechanical issue in a diesel engine," said a statement from US Central Command (CENTCOM), and both vessels stopped.
"This stop occurred in Iranian territorial waters, although it's not clear the crew was aware of their exact location. While the RCBs were stopped and the crew was attempting to evaluate the mechanical issue, Iranian boats approached the vessels."
CENTCOM said that there was soon four Iranian vessels at the scene, all with armed personnel aboard and after a conversation between the two sides armed Iranian military boarded the RCBs.
Meanwhile, Iranian personnel on their own vessels kept watch with mounted machine guns and the US boats were then escorted at gunpoint to Farsi Island.
"A post-recovery inventory of the boats found that all weapons, ammunition and communication gear are accounted for minus two SIM cards that appear to have been removed from two handheld satellite phones," said the US Central Command, which oversees US operations in the Middle East.