“Moussa Faki Mahamat strongly condemns the continued air strike attacks by Israel on Gaza that have killed more than 30 Palestinian civilians, including 6 children,” an AU statement said.
The “targeting of civilians and the continued illegal occupation by Israeli security forces of the Occupied Territories, are in stark violation of international law, and complicate the search for a just and lasting solution”, the statement said.
The new fighting is the worst to hit Gaza since last year's conflict, which left the 2.3 million Palestinians living there in poverty and compelled Israelis to seek cover from rockets.
Israel has increased its rocket attacks on Islamic Jihad positions, a group sponsored by Iran that has been labelled a terrorist organisation by a number of Western countries. In response, the militants have launched over 500 missiles.
Powerful member states, most notably South Africa, have been vocal in their opposition to Faki's decision last year to accept Israel's accreditation to the bloc as an observer, making the relationship with Israel a rare topic of dispute for the AU, an organisation that prizes unanimity.
Although the decision was a significant diplomatic victory for Israel, criticising member states claimed it went against prior AU pronouncements supporting the Palestinian Territories, including those made by Faki himself.
The AU reaffirmed its support for "the Palestinian people in their legitimate desire for an independent and sovereign State" with East Jerusalem as its capital in a statement released on Sunday.