His allegations on Monday came at the start of a meeting with Antonio Guterres, the United Nations secretary-general, who is on his first official visit to the region since taking office at the beginning of the year.
"Iran is busy turning Syria into a base of military entrenchment, and it wants to use Syria and Lebanon as war fronts against its declared goal to eradicate Israel," Netanyahu said in Tel Aviv, without offering anything to support his allegations.
"[Iran] is also building sites to produce precision-guided missiles towards that end in both Syria and in Lebanon," he said, without offering specifics. "This is something Israel cannot accept. This is something the UN should not accept."
There was no immediate comment from Tehran.
Both Iran and Lebanese movement Hezbollah have backed Syrian President Bashar al-Assad's government forces in the civil war that has ravaged Syria.
Netanyahu pressed Guterres on the UN peacekeeping force in neighbouring Lebanon, known as UNIFIL, with Israeli officials having accused it of "blindness" to what they call an arms build-up by Hezbollah.
Guterres vowed that he will "do everything in my capacity" to ensure UNIFIL fulfils its obligations.
The UN Security Council is debating a renewal of the force's mandate for a year, with a vote expected on Wednesday.
Guterres arrived on Sunday for a three-day visit to the region at a tense time between Israel and the UN.
In July, UNESCO listed the Old City of Hebron in the West Bank as an endangered Palestinian world heritage site. The move prompted anger in Israel and led to Netanyahu slashing the UN membership that his country contributes by $10m.
At a joint press conference with Guterres, Netanyahu said his country has been treated unfairly and urged Guterres to address the issue.
"There is no question that we've had a troubled relationship with the UN," Netanyahu said.
"I think it has an absurd obsession with Israel, flagrantly discriminatory tactics - you don't have to be the Israeli prime minister to understand that."
For his part, Guterres made a forceful argument for a two-state solution with the Palestinians and spoke of what he called obstacles to peace, including Israeli settlement building.
"I dream that I will have the chance to see in the Holy Land two states able to live together in mutual recognition, but also in peace and security," Guterres said in remarks at Netanyahu's office, calling for an improvement of economic and social conditions for Palestinians.
He also vowed to use his position to combat all forms of racism and bigotry and said that those who call for Israel's destruction peddle in a "form of modern anti-Semitism" - though he added that he does not always agree with the country's policies.
"Guterres wishes to be both impartial and a messenger of peace," said Al Jazeera's Harry Fawcett, reporting from West Jerusalem.
"He is in favour of a two-state solution and one in which the Palestinians would see an improvement in their economic and social well-being so that they would have a stake in peace going forward."
Guterres is due in Ramallah on Tuesday for talks with Palestinian Prime Minister Rami Hamdallah.
Palestinian President Mahmoud Abbas is visiting Turkey and is not expected to meet Guterres during the trip.
Guterres will then travel to the Gaza Strip on Wednesday, where the issue of a crippling electricity crisis will be on the agenda.
Al Jazeera's Fawcett said the issue of Gaza's power crisis will be on the agenda.
Palestinians have been calling on Guterres to keep up the pressure on illegal Israeli settlements in the occupied West Bank.
Yet, senior Palestinian officials are expressing concerns "that Guterres may not be the vociferous proponent of changing Israel's policy", Al Jazeera's Fawcett said.
Hanan Ashrawi, member of the Palestinian Liberation Organisation, echoed those fears.
"Guterres whom we've known for years and we had hoped would signal a new will on the part of the UN leadership to stand up to Israel, we’re beginning to see not just a regression, a sense of intimidation and reticence when it comes to Israel," she said.
Source: Al Jazeera and news agencies