Two warning shots were fired at the 11-storey Jalaa building in central Gaza City, housing local and international media as well as private apartments, an AFP correspondent reported.
"Two very precise shots were fired straight into our building," said Al-Jazeera reporter in Gaza Stefanie Dekker, according to the channel's English-language website.
The empty missiles were directed at Al-Jazeera's office, prompting journalists, along with a number of families who had sought refuge there from Sunday's fighting in Shejaiya, to leave.
"We came here from Shejaiya," said a woman standing outside with three female relatives, nine children and an elderly man. "There doesn't seem to be anywhere that is safe."
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Elsewhere in the city, rescue teams were seen outside the 10-storey Salaam tower block which was hit a day earlier, causing the top five floors to cave in on themselves.
Towards the top, a dusty limb could be seen sticking out from under a large piece of rubble, which had trickles of dried blood on it.
The pan-Arab Al-Jazeera channel has offered extensive coverage from Gaza since Israel began its military campaign against the Hamas-controlled coastal strip on July 8.
Ynet news website quoted Israeli Foreign Minister Avigdor Lieberman as saying on Monday that Al-Jazeera "stands at the heart of the propaganda of terrorist organisations".
Al-Jazeera accused Lieberman of "direct incitement" against it.
The channel is funded by gas-rich Qatar, which backs the Islamist Hamas movement.