"A mortar round was fired at forces during operational activity adjacent to the security fence in the southern Gaza Strip," the Israeli army said in a statement.
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"A... tank responded and fired towards the threat."
A Palestinian security source in the Hamas-run territory confirmed the Israeli fire but not the mortar attack.
The source said two shells were fired at a site under the control of the interior ministry in the south of the enclave, causing damage but no casualties.
Despite Israeli allegations that Hamas is building fresh tunnels that could reach into Israel, the border region has remained relatively quiet in recent months.
The tunnels were cited by Israel as a key cause of its summer 2014 war in Gaza, which killed 2,251 Palestinians, mostly civilians, and 73 Israelis, including 67 soldiers, according to the United Nations.
The ceasefire which ended the conflict has been sporadically threatened by rocket fire from Gaza.
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Most of it has been attributed to fringe Islamist groups challenging Hamas's authority, although Israel holds Hamas responsible for all rocket fire from the territory and routinely responds with attacks on its positions.
During a visit to the Gaza border on Tuesday, Prime Minister Benjamin Netanyahu hailed its calmest period in years, according to comments reported by Israeli media.
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