"For the first time since operation Protective Edge, a mortar shell fired from Gaza hit southern Israel," Lieutenant Colonel Peter Lerner said on Twitter, referring to the military offensive in Gaza.
"No damage or injuries reported," he added.
In Gaza, a spokesperson for Hamas, the strip's de facto rulers, told AFP that the militant group and others wanted the three-week old ceasefire to hold.
"The Palestinian factions are committed to the truce," Sami Abu Zuhri said. "We want it to continue."
He questioned whether the attack as reported by Israel had in fact taken place.
"There is no evidence that there was mortar fire from the Gaza Strip," he said.
An Israeli army statement said that the mortar round fell in the Eshkol region, which borders the Gaza Strip.
In July, Israel launched the operation with the declared aim of halting rocket fire from the Gaza Strip. An ensuing 50-day war with militants killed at least 2,143 Palestinians, nearly 70 percent of them civilians, and 73 people on the Israeli side.
The sides, working through Egyptian mediators, are supposed to start negotiations in Cairo this month to agree a more formal and long-term version of the existing open-ended truce.
Earlier Tuesday, Israel confirmed that it had signed up to a United nations-brokered deal to facilitate reconstruction of the shattered coastal strip while keeping materials out of the hands of Hamas militants.
"Israel has agreed to the proposal of the United Nations to establish a mechanism for rehabilitation of the Gaza Strip under the supervision and control of the UN," the defence ministry's department for civil affairs in the Palestinian territories said.
"The mechanism will facilitate progress in rebuilding the Gaza Strip while safeguarding the security interests of the state of Israel."
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