Agency spokesman Mahmud Basal said the military used loudspeakers on drones to tell displaced people sheltering in a school to leave, while also firing tank shells at the area.
The army's "aerial and artillery" fire forced thousands to flee Beit Lahia via Salah al-Din road, Gaza's main north-south axis, he told AFP.
The Israeli military did not immediately respond to a request for comment.
An Israeli military official speaking on condition of anonymity denied reports there were no civilians remaining in northern Gaza.
Zudi Agha, 45, said he was displaced from his home in Beit Lahia to the school but fled for Al-Saftawi, near Gaza City.
He said shooting began the night before, while at dawn drones with speakers told them to "leave the school and the area to save your lives".
The violence intensified in the morning, said Agha.
"I saw people fleeing so I decided to escape," he said. "We walked and carried my mother on a donkey cart. There were tanks everywhere and the whole area was rubble and destruction."
'Dozens of bodies'
The military frequently issues evacuation calls in northern Gaza where, since October 6, it has pressed a major offensive it says is aimed at stopping Hamas from regrouping.
The operation began in the city of Jabalia before expanding to include Beit Lahia.
Ghadeer al-Bardai, 24, said he also fled the area.
"Whoever stays will be sentenced to death," he said, adding he saw "dozens of bodies" on the road out of Beit Lahia.
"Every day, (Israel) bombs and bulldozes homes and buildings and destroys all the necessities of life... The northern Gaza Strip has become a ruin and rubble," he told AFP.
On Tuesday, the UN's humanitarian agency OCHA said an emergency medical team was successfully deployed to Kamal Adwan hospital in Beit Lahia for the first time in 60 days.
It said 65,000-75,000 people had been left "without access to food, water, electricity or reliable health care" by the Israeli operation in northern Gaza, "as mass casualty incidents continue".
World Health Organization head Tedros Adhanom Ghebreyesus said, in a post on X, that Kamal Adwan hospital was "attacked again last night", adding that such actions were "depriving people of lifesaving care".
The war began on October 7, 2023, sparked by Hamas's unprecedented attack on Israel that resulted in the deaths of 1,208 people, mostly civilians, according to an AFP tally based on official data.
Israel's retaliatory military campaign in Gaza has resulted in at least 44,532 deaths, mostly civilians, according to data from the territory's Hamas-run health ministry, which the UN considers reliable.
