U.N. aid agencies plan to begin a massive vaccination drive across Gaza on Sunday to try to protect young children from a rare type of polio, having persuaded Israel to pause combat operations for several hours a day in certain locations.

The effort faces enormous logistical challenges in a war zone where much of the infrastructure has been destroyed. The operation depends on the brief cease-fires holding while rule of law has broken down, hundreds of thousands are living in temporary shelters and many buildings are in ruins.

But it comes too late for at least one infant boy who was diagnosed with poliovirus type-2 earlier this month — the first confirmed case of the disease to surface in Gaza after it was eradicated in most of the world during the 1990s.

The World Health Organization and UNICEF, the U.N. children’s fund, have delivered more than 1.2 million doses of polio vaccination from Indonesia to distribute to about 640,000 children in Gaza under 10 years old. Another 400,000 doses are on their way.

At least 90 percent of those children need to be vaccinated to stop the disease from spreading, Dr. Rik Peeperkorn, the top W.H.O. representative in Gaza, told reporters on Thursday.

That will take a force of about 2,100 health and community aid workers in Gaza, at some 700 medical facilities, mobile clinics and shelters. They will administer the polio vaccination during a staggered pause in military operations for nine hours a day for three days in designated areas in each of Gaza’s three main regions — north, south and central.