However, he said he is still trying to minimise the impact of the dispute on his country's relations with the United States.
"We do have today a profound disagreement with the United States administration and the rest of the P5+1 over the offer that has been made to Iran," Netanyahu's office quoted him as saying.
Iran and Britain, China, France, Russia, the United States and Germany have been seeking a comprehensive accord that would prevent Tehran from developing a nuclear bomb in return for an easing of economic sanctions.
In his statement, Netanyahu said what the P5+1 was offering in the negotiations "would enable Iran to threaten Israel's survival."
"This is a regime, Iran, that is openly committed to Israel's destruction," he said.
"It would be able, under this deal, to break out to a nuclear weapon in a short time, and within a few years, to have the industrial capability to produce many nuclear bombs for the goal of our destruction."
Obama has refused to meet Netanyahu during his trip to Washington next month, saying diplomatic protocol forbade him from doing so, as the Israeli leader is fighting for re-election on March 17.
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"This is not a personal disagreement between President Obama and me. I deeply appreciate all that he has done for Israel in many fields," said Netanyahu.
"Equally, I know that the president appreciates my responsibility, my foremost responsibility, to protect and defend the security of Israel.
"I am going to the United States not because I seek a confrontation with the president, but because I must fulfil my obligation to speak up on a matter that affects the very survival of my country.
"I intend to speak about this issue before the March 24th deadline and I intend to speak in the US Congress because Congress might have an important role on a nuclear deal with Iran."
Some lawmakers are threatening to seek new sanctions on Tehran.
Iran denies seeking an atomic bomb and says its nuclear programme is for peaceful energy purposes only.
President Hassan Rouhani said Tuesday that world powers must "seize the opportunity" of a nuclear deal, insisting Tehran had taken the "necessary steps" for an accord.
Two deadlines for a permanent agreement on Iran's nuclear programme have already been missed, requiring the talks to be extended.
Negotiators are now working toward the political outline of a deal by March 31, with the cut-off point for the technical details of a comprehensive accord by June 30.