The shots caused panic among the civilians living in the same building but no casualties have been reported, Al Jazeera reported.
"Two very precise shots were fired straight into our building," Al Jazeera's Stephanie Dekker, reporting from the bureau in Gaza, said.
"We are high up in the building so we had a very strong vantage point over the area. But we have evacuated."
The bureau is situated in a residential area of Gaza City.
Al Jazeera has been covering the Israeli offensive on the Gaza Strip that started July 8.
The death toll in Israel's 14-day assault has escalated to over 500 Palestinians, including women and children.
More than 3,600 others have been injured.
On the Israeli side, 27 security personnel and two civilians have been killed.