A red-faced Pentagon has conceded that an instructor at its Joint Forces College in Virginia for military officers was until recently teaching a course advocating “total war” with Islam that could require obliterating the holy cities of Mecca and Medina without concern for civilian deaths.

The material in the course, which officers could elect to take but was not obligatory, flew in the face of repeated assertions by the Obama administration that the war on terrorism is just that and should under no circumstances be read as an assault on a religion observed by 1.4 billion people around the world.

Details of the course were obtained by a blog on Wired.com, drawn from a presentation given by the teacher, Lt. Col. Matthew Dooley, in July last year. He suggested that destroying Islamic holy sites would follow the precedents of the nuclear strike by the allies on Hiroshima in World War II and the firebombing of Dresden. His course was called ‘Perspectives on Islam and Islamic Radicalism’.

It was suspended in April after the Pentagon received a complaint from a student and Lt. Col. Dooley, while still at the College, no longer has any teaching duties. The FBI, meanwhile, has revealed that it too has recently been forced to revise some of its instructional materials to excise references that could have been insulting to Islam.

“It was just totally objectionable, against our values, and it wasn't academically sound,” the Chairman of the Joint Chiefs, General Martin Dempsey, said at a press conference at the Pentagon. “This wasn't about ... pushing back on liberal thought; this was objectionable, academically irresponsible.”

Dooley offered a theoretical war plan based on the need for “a direct ideological and philosophical confrontation with Islam”. In his presentation, he said: “They hate everything you stand for and will never coexist with you, unless you submit”. He added that as America waged that war it would be free to ignore provisions of the Geneva Convention that sets the rules for armed conflict as “no longer relevant”.

“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...).” Saying Islam has already declared war on the US, Dooley called the current American stance of seeking common ground with Islamic leaders around the world as “illogical” and the better option was “waging ‘near total war’”.

“We have now come to understand that there is no such thing as ‘moderate Islam’,” Dooley said in the July presentation. “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.”