According to the survey, the American disapproval ratings are as high as 64 percent in Pakistan and 77 percent in the Palestinian territories.
Majorities in six of the seven Muslim nations surveyed feel the US is a military threat to their country.
Though respondents in most countries thought Obama will take a multilateral approach to foreign policy and be fair in his dealings with the Israelis and Palestinians, Muslim nations thought otherwise.
In the Palestinian territories, Jordan, Egypt, and Lebanon, more than six-in-ten doubted whether Obama will be fair on the Middle East issues, according to the survey.
However, the US ratings are up to 61 percent among Muslims in Nigeria in Africa -- the continent where Obama's Kenyan Muslim father came from -- and 63 percent in Indonesia where Obama spent many years as a child.
While Indonesia is the world's biggest Muslim nation, Muslims constitute 50 percent of the Nigerian population.
But what was surprising was a 90 percent approval rating for the US among Lebanon's Sunni Muslims as against just two percent among Lebanese Shias who are aligned with Shiite Iran and Syria.
The survey said Obama's election may not have brought about a sea change in Muslim attitudes towards the US, but he may be laying the groundwork for improvement.