Israeli military says "it was not a projectile launch" or other fire that posed a threat to its residents or illegal settlers.
The Israeli army said it has "intercepted a small aircraft over the Gaza Strip", where witnesses told the AFP news agency they heard "explosions" near the fence.
The army on Saturday stressed it was not rocket or other fire that posed a threat to Israelis.
"It was not a projectile launch. Full routine continues on the Israeli home front," it said in a statement.
There was no immediate claim of responsibility from Gaza's Hamas government or any of the armed Palestinian factions.
Earlier on Saturday, the Gaza-based Islamic Jihad group said its leader Ziad al Nakhala had travelled to Cairo to meet Egyptian intelligence chief Abbas Kamel.
It said the two sides discussed "the situation in Jerusalem, and the West Bank, especially Jenin," a flashpoint city and refugee camp, where Israel last month conducted its deadliest single operation in the occupied West Bank in years, killing 10 people.
The trip followed a visit by Kamel to the West Bank city of Ramallah on Tuesday, where he met Palestine's President Mahmud Abbas to discuss the recent surge in violence.
Since the start of the year, the conflict over Israeli occupation of Palestinian lands has claimed the lives of 36 Palestinians.
Six Israelis and one Ukrainian civilian have been killed over the same period.
Millions under occupation
The densely populated Gaza, which is home to 2.3 million Palestinians, has been under Israeli blockade from land, air and sea, since 2005.
Israel occupied the West Bank, including East Jerusalem, and Gaza during the 1967 Arab-Israeli War. It annexed the entire East Jerusalem city in 1980.
Palestine sees East Jerusalem, along with Gaza, as part of the country with East Jerusalem as the capital.
Under international law, the West Bank and East Jerusalem are "occupied territories" and all Jewish settlement-building activities on the land are illegal.
Palestinians accuse Israel of waging an aggressive campaign to "Judaise" the historic city by effacing its Palestinian Arab and Islamic identity and driving out its Palestinian inhabitants.
Almost 500,000 illegal Israeli settlers live in over 130 settlements dotting the occupied West Bank alongside nearly three million Palestinians living under Israeli military occupation.