Netanyahu made the comments from the summit of Mount Hermon — the highest peak in the area — inside Syria, about 10km from the border with the Israel-held Golan Heights.
It appeared to be the first time a sitting Israeli leader had set foot that far into Syria.
Israel's capture of the buffer zone, a demilitarised area in Syria, has sparked condemnation (AP PHOTO)
Netanyahu said he had been on the same mountaintop 53 years ago as a soldier, but the summit's importance to Israel's security has only increased given recent events.
Israel seized a swath of southern Syria along the border with the Israeli-annexed Golan Heights days after Assad was ousted by rebels last week.
Israel's capture of the buffer zone, a roughly 400sq/km demilitarised area in Syrian territory, has sparked condemnation, with critics accusing Israel of violating a 1974 ceasefire and possibly exploiting the chaos in Syria in the wake of Assad's ouster to make a land grab.
"We will stay ... until another arrangement is found that ensures Israel's security," said Netanyahu who had travelled to the buffer zone on Tuesday with Defence Minister Israel Katz.
Katz said he instructed the Israeli military to quickly establish a presence, including fortifications, in anticipation of what could be an extended stay in the area
"The summit of the Hermon is the eyes of the state of Israel to identify our enemies who are nearby and far away," he said.
An Israeli military official, who spoke on condition of anonymity in line with military regulations, said there is no plan to evacuate the Syrians living in villages within the buffer zone.
The buffer zone between Syria and the Israeli-controlled Golan Heights was created by the UN after the 1973 Mideast war. A UN force of about 1100 troops had patrolled the area since then.
A UN spokesman said on Tuesday that the advance of Israeli troops, however long it lasts, violates the deal that set up the buffer zone.
That agreement "needs to be respected, and occupation is occupation, whether it lasts a week, a month or a year, it remains occupation," spokesman Stephane Dujarric said.
There was no immediate comment from Hayat Tahrir al-Sham, the insurgent group that led the ouster of Assad, or from Arab states.
Israel still controls the Golan Heights, which it captured from Syria during the 1967 Mideast war and later annexed — a move not recognised by most of the international community. Mount Hermon's summit is divided between the Israeli-annexed Golan Heights, Lebanon, and Syria.
Only the United States recognises Israel's control of the Golan Heights.
The bodies of more than 30 Syrians who vanished under Assad's rule were uncovered in a mass grave. (AP PHOTO)
With Assad gone, a top US official said that militant leaders who have taken over Syria have committed to "an ambitious scaling-up of vital humanitarian support" for millions in desperate need of food and other aid.
In other developments, bodies of more than 30 Syrians who vanished under Assad's rule were uncovered in a mass grave on Monday.
Forensic teams and rebels worked together to unearth the remains in the village of Izraa, north of the city of Daraa, as families of the missing stood by.
The relatives said they had initially hoped to find their loved ones in prison.
"But we didn't find anyone and it broke our hearts. They were burned alive here after being doused in fuel," said Mohammad Ghazaleh, who was waiting at the mass grave site.
