Petraeus said that the worsening conflict "weakens the legitimacy of moderate regimes in the Arab world".
He also said al-Qaeda and other groups sought to "exploit" Arab anger over the issue and that the conflict "gives Iran influence in the Arab world" through its "clients" Hamas in the Palestinian territories and Hezbollah in Lebanon.
Petraeus' comments highlight concerns among senior US officers as they draw down US forces in Iraq, increase the number in Afghanistan and prepare for a possible showdown with Iran over its nuclear programme.
They come amid one of the worst public disagreements between Israel and the US over Israel's announcement that it would build 1,600 new housing units in a Jewish settlement in an area of east Jerusalem by Israel.
Senior administration officials, including Hillary Clinton, the secretary of state, and David Axelrod, an adviser to President Barack Obama, have called the timing of the announcement – made during a visit by Joe Biden, the vice-president - insulting and destructive to US efforts to broker peace.
Petraeus told Admiral Mike Mullen, the chairman of the joint chiefs of staff, that the process, which has been further stalled by the Israeli move, was hurting Washington's credibility in the region.
"My thrust has generally been, literally, just to encourage that process that can indeed get ... a sense of progress moving forward in the overall peace process because of the effect that it has on particularly what we would term the 'moderate' governments in our area," he said in his statement.