A senior Israeli military official said it would not apply to the town of Rafah and that Israeli troops would respond if they were attacked.
Earlier, United Nations chief Ban Ki-moon described an Israeli strike near a UN-run school in Gaza as “a moral outrage and a criminal act”.
Palestinian officials said at least 10 people died in the attack on Sunday.
The Israel Defense Forces (IDF) confirmed on Sunday that they had begun withdrawing some troops from Gaza, saying it was “extremely close” to completing its mission to destroy a network of tunnels.
Health officials in Gaza say 1,800 Palestinians, most of them civilians, have been killed and more than 9,000 injured since the conflict began nearly four weeks ago.
Sixty-six Israelis have died, all but two of them soldiers. A Thai national working in Israel was also killed.
In the outrage that followed Sunday’s attack on the UN school, Israel announced it would hold a “humanitarian window” in its Gaza offensive to allow hundreds of thousands of displaced Palestinians to return to their homes.
The ceasefire would not include Rafah because there was an “Israeli military presence” there and “clashes were still ongoing”, an IDF statement said.
It said the truce would last from 10:00 local time (07:00 GMT) until 17:00 (14:00 GMT).
The Israeli army warned that it would “respond to any attempt to exploit this window” by Islamist militants in Gaza.
Hamas responded to the truce with suspicion and its spokesman, Sami Abu Zuhri, accused the IDF of attempting to “divert the attention from Israeli massacres.”
Source: BBC