A course for US military officers has been teaching that America’s enemy is Islam in general and suggesting that the country might ultimately have to obliterate the Islamic holy cities of Mecca and Medina without regard for civilian deaths, following second world war precedents of the nuclear attack on Hiroshima.

The Pentagon suspended the course in late April when a student objected to the material. The FBI also changed some agent training last year after discovering that it, too, was critical of Islam.

The teaching in the military course was counter to repeated assertions by US officials over the past decade that America is at war against Islamic extremists, not the religion itself.

“They hate everything you stand for and will never coexist with you, unless you submit,” the instructor, Lieutenant Colonel Matthew Dooley, said in a presentation last July for the course at Joint Forces Staff College in Norfolk, Virginia. The college, for professional military members, teaches mid-level officers and government civilians on subjects related to planning and executing war.

Dooley also presumed, for the purposes of his theoretical war plan, that the Geneva conventions that set standards of armed conflict, are “no longer relevant”.

He adds: “This would leave open the option once again of taking war to a civilian population wherever necessary (the historical precedents of Dresden, Tokyo, Hiroshima, Nagasaki being applicable to the Mecca and Medina destruction decision point).”

His war plan suggests possible outcomes such as “Saudi Arabia threatened with starvation … Islam reduced to cult status”.

A copy of the presentation was obtained and posted online by Wired.com’s Danger Room blog . The college did not respond to the Associated Press’ requests for copies of the documents, but a Pentagon spokesman authenticated the documents. Dooley still works for the college, but is no longer teaching, said the joint chiefs of staff chairman, General Martin Dempsey. Dooley has refused to comment.

A military service record summary provided by army human resources at Fort Knox, Kentucky, shows that Dooley was commissioned as a second lieutenant upon graduation from the US military academy at West Point, New York, in May 1994. He has served tours in Germany, Bosnia, Kuwait and Iraq. He has numerous awards including a Bronze Star medal, the fourth-highest US combat award.

In what he termed a model for a campaign to force a transformation of Islam, Dooley called for “a direct ideological and philosophical confrontation with Islam”, with the presumption that Islam is an ideology rather than just a religion.

He further asserted that Islam has already declared war on the west, and the US specifically.

“It is therefore illogical” to continue with the current US strategy, which Dooley said presumes there is a way of finding common ground with Islamic religious leaders, without “waging near total war”.

The course on Islam had been taught since 2004, but was not part of the required core curriculum. It was offered five times a year, with about 20 students each time.

Though Dooley has been teaching at the college since August 2010, it was unclear when he took on that particular class, called Perspectives on Islam and Islamic Radicalism.

The joint staff suspended the course after it had received a student complaint, and within days Dempsey ordered all service branches to review their training to ensure other courses do not use anti-Islamic material.

On Thursday, Dempsey said the material in the Norfolk course was counter to American “appreciation for religious freedom and cultural awareness”.

“It was just totally objectionable, against our values, and it wasn’t academically sound,” Dempsey said. “This wasn’t about … pushing back on liberal thought; this was objectionable, academically irresponsible.”

In his July 2011 presentation on “counterjihad”, Dooley asserted that the rise of what he called a “military Islam/Islamist resurgence” compels the US to consider extreme measures, “unconstrained by fears of political incorrectness”.

He described his purpose as generating “dynamic discussion and thought”, while noting that his ideas and proposals are not official US government policy and cannot be found in any current official defence department documents.

A Pentagon inquiry is seeking to determine whether someone above the professor’s level is supposed to approve course materials and whether that approval process was followed in this case, said Colonel Dave Lapan, a spokesman for Dempsey.

The problem of negative portrayals of Islam in federal government is not new. A six-month review the FBI launched into agent training material uncovered 876 offensive or inaccurate pages that had been used in 392 presentations, including a PowerPoint slide that said the bureau can sometimes bend or suspend the law in counterterror investigations.