Gen Martin Dempsey has now ordered a full investigation into the course America's top military officer has condemned a course taught at a US military college that advocated a "total war" against Muslims.
The Chairman of the Joint Chiefs of Staff, Gen Martin Dempsey, said the course was "totally objectionable" and "against our values".
The voluntary course at the Joint Forces Staff College in Virginia also suggested possible nuclear attacks on holy Muslim cities such as Mecca.
The course has now been suspended. "It was just totally objectionable, against our values, and it wasn't academically sound," Gen Dempsey said.
He added that he had ordered a full investigation when the course was suspended in April after one of the students objected to the material.
The officer in charge of the class, Lt Col Matthew Dooley, has been suspended from teaching but has kept his job at the college in the city of Norfolk.
The Pentagon has also confirmed that the course material found on their website is authentic.
The story broke after a copy of the presentation of the course material was posted online by Wired.com's Danger Room blog.
"We have now come to understand that there is no such thing as 'moderate Islam'," Lt Col Dooley said in the presentation last July.
"It is therefore time for the United States to make our true intentions clear. This barbaric ideology will no longer be tolerated. Islam must change or we will facilitate its self-destruction."
He added that international laws protecting civilians in armed conflicts - such as the Geneva Conventions were "no longer relevant".
That left open the option, the instructor continued, of applying "the historical precedents of Dresden, Tokyo, Hiroshima, Nagasaki" to Islam's holiest cities, and bringing about "Mecca and Medina destruction".
Lt Col Dooley has made no public comments on the issue since the story broke.
The Pentagon hopes a full report will be out by the end of the month, the BBC's North America editor Mark Mardell reports.
What does seem rather surprising, he adds, is that all those commanders, captains and colonels must have sat through the course and not felt the need to tell someone that something rather weird was going on.
BBC © 2012
يَا أَيُّهَا الَّذِينَ آمَنُوا لَا تَتَّخِذُوا بِطَانَةً مِّن دُونِكُمْ لَا يَأْلُونَكُمْ خَبَالًا وَدُّوا مَا عَنِتُّمْ قَدْ بَدَتِ الْبَغْضَاءُ مِنْ أَفْوَاهِهِمْ وَمَا تُخْفِي صُدُورُهُمْ أَكْبَرُ قَدْ بَيَّنَّا لَكُمُ الْآيَاتِ إِن كُنتُمْ تَعْقِلُونَ
"O you who believe! Take not as (your) Bitanah (advisors, consultants, protectors, helpers, friends, etc.) those outside your religion (pagans, Jews, Christians, and hypocrites) since they will not fail to do their best to corrupt you. They desire to harm you severely. Hatred has already appeared from their mouths, but what their breasts conceal is far worse. Indeed We have made plain to you the Ayat (proofs, evidences, verses) if you understand." Quran 3:118
Wake Up, Oh Muslim Ummah!!