The campaign, in coordination with the UN, will last 12 days in total.
The decision to stop the oral vaccine is in accordance with World Health Organization policy.
More than 446,000 Palestinian children in central and south Gaza were vaccinated earlier this month.
The campaign in north Gaza aims to conclude a first vaccination round, with a second set to commence after a month.
UNRWA's Philippe Lazzarini later commented on the incident on social media, claiming that the IDF had stopped the personnel for over eight hours.
Vaccine pauses in Gaza’s polio crisis aren’t political—they're vital for public health.
That amounts to about a quarter of the total population targeted in the campaign to stop the spread of the disease, which can cause paralysis and even death in young children.
The PMO stressed that Israel is committed to preventing an outbreak of the disease in the Gaza strip, as well as in the entire region.
A recent detection of type 2 polio in a Gaza infant marks the first case in 25 years, sparking concern over a potential outbreak.
The operation was conducted in conjunction with COGAT and under the political echelon's directives.