Ban met in Baghdad with Iraqi Prime Minister Nouri al-Maliki. Recent internal divisions and growing acrimony with Turkey have raised concerns about Iraq's post-war stability.
Bruce Riedel, a former CIA analyst who studies terrorism at the Brookings Institution, told The Washington Post this week that he saw signs of an al-Qaida "revival" in Iraq.
Ban, in an address, said divisions among Shiites, Sunnis and ethnic Kurds was a "disservice to the people of Iraq, who look to their leaders to deliver a better future."
Iraq announced recently it would have provincial council elections in April. Elections in 2009 resulted in the longest political stalemate in world history as Iraq's leaders struggled to reconcile over their internal differences.
Ban said there is "no alternative" in Iraq apart from one that is united.
"Above all, I worry that increased political polarization could stoke sectarian violence and reverse the precious security gains against terrorism in recent years," he said.