"Israel is a vibrant democracy and I do not believe, not have I ever stated, publicly or privately that Israel is an apartheid state or that it intends to become one," the top US diplomat said in a strong statement after calls earlier in the day for him to resign or at least apologise for the alleged comments.
"Anyone who knows anything about me knows that without a shred of doubt."
But Kerry, who has seen his dogged efforts to broker peace between Israel and the Palestinians collapse, did suggest that he had used a poor choice of words during his speech on Friday to international experts of the Trilateral Commission.
"I have been around long enough to also know the power of words to create a misimpression, even when unintentional, and if I could rewind the tape, I would have chosen a different word to describe my firm belief that the only way in the long term to have a Jewish state and two nations and two peoples living side by side in peace and security is through a two-state solution."
The Daily Beast online news site reported that Kerry had warned that "a unitary state winds up either being an apartheid state with second-class citizens - or it ends up being a state that destroys the capacity of Israel to be a Jewish state".
The website said it had been given a recording of Kerry's speech, which sparked a furore in Israel and led one Republican senator to call for his resignation.
Kerry has "repeatedly demonstrated a willingness to countenance a world in which Israel is made a pariah," said Senator Ted Cruz.
"Before any more harm is done to our national security interests and our critical alliance with the state of Israel," Kerry should offer his resignation and President Barack Obama should "accept it," he added.
Veteran Republican Senator John McCain also said Kerry should clarify his comments immediately and apologise, but laughed at the suggestion the top US diplomat should step down.
In his statement, Kerry said: "I will not allow my commitment to Israel to be questioned by anyone, particularly for partisan, political purposes."
He insisted that "for more than thirty years in the United States Senate, I didn't just speak words in support of Israel, I walked the walk when it came time to vote and when it came time to fight."
He also said that in his year in office as secretary of state, he had "spent countless hours" working with Israeli Prime Minister Benjamin Netanyahu and Justice Minister Tzipi Livni, who is Israel's lead negotiator, "because I believe in the kind of future that Israel not only wants, but Israel deserves.
"I want to see a two state solution that results in a secure Jewish state and a prosperous Palestinian state, and I've actually worked for it."