In a new message posted on the Internet, Ayman Al-Zawahiri claimed Obama has brought the region nothing but "blockade and siege" despite efforts to reach out to Arabs.
"Obama's plan, though wrapped in smiles and calls for respect and understanding, aims only to support Israel," al-Zawahiri said in a 26-minute audio message.
Usama bin Laden's deputy has been critical of Obama since his election, even releasing a message that referred to the U.S. president as a "house negro," a slur for a black subservient to whites.
"Obama's policy is nothing but another cycle in the Crusader and Zionist campaign to enslave and humiliate us, and to occupy our land and steal our wealth," al-Zawahiri said.
The authenticity of the statement could not be independently verified, but it was posted on a Web site commonly used for militant messaging.
In it, al-Zawahiri also scoffed at key American allies in the region — the Egyptian president and the Jordanian and the Saudi kings — for supporting peace with Israel.
He urged Muslims and Palestinians to wage holy war, or jihad, not only in Israel and the Palestinian territories but also beyond those areas, saying there are "ample opportunities elsewhere."
He praised Muslim militants fighting in Pakistan, saying the conflict there was a "war of Muslim dignity and pride" and warned the Palestinians against any negotiations with Israel.
"We should continue jihad to liberate Palestinian land and establish an Islamic state there. We should wage jihad against Jews and all those who support them, whether they are Americans or Westerners," he said.
The terror network's No. 2 said the group "will not forget" its members held in American prisons.
He specifically mentioned Ramzi Youssef, convicted and now serving a life sentence for the first World Trade Center attack in 1993, and also Khalid Sheikh Mohammed, Al Qaeda's mastermind of the September 11 bombings.
Mohammed and four others, held for years at the military base in Guantanamo Bay, are due to stand trial on charges they plotted the September 2001 attacks that killed nearly 3,000 people.