In the statement released by the ministry, which is run by the Islamic Resistance Movement (Hamas), two Palestinian men were killed and five civilians were injured in the attacks on the Al-Nasser neighborhood.
The ministry identified the victims as PIJ militants Eyad Al-Hasani and Mohamed Abdel Aal.
According to a statement released by the Israeli Defense Forces (IDF), Eyad Al-Hasani was "a significant figure in leading the operations and making military decisions" of the PIJ.
"Al-Hasani was a key figure in the organization and was involved in all decisions regarding rocket launches and barrages toward Israel," the IDF statement read.
The PIJ’s armed wing said in a statement that "assassinating our leaders won’t stop our resistance."
According to the health ministry, 33 people have been killed and more than 100 others injured since Israel began airstrikes on the PIJ’s armed wing on Tuesday.
On Tuesday, Israeli fighter jets and unmanned drones carried out simultaneous and surprising airstrikes against buildings and apartments that host senior PIJ military leaders in the Gaza Strip.
On Wednesday afternoon and Thursday, the PIJ militants fired more than 500 rockets at central and southern Israel, leaving one Israeli woman killed and more than nine injured, according to Israeli media reports.
Palestinian sources said that Egypt, Qatar, and the UN have so far failed to mediate a ceasefire between Israel and the Hamas-led militant groups, including the PIJ.