Alex Younger said that while Ian Fleming's famous character had helped popularise Britain's secret service brand, it bore no resemblance to reality.
Younger, the 16th chief since MI6 was founded in 1909, is known as "C", rather than "M" as in the Bond films.
"I am conflicted about Bond. He has created a powerful brand for MI6: as C, the real-life version of M, there are few people who will not come to lunch if I invite them. Many of our counterparts envy the sheer global recognition of our acronym," Younger said.
C is the only member of MI6 who can be publicly identified.
"The risks at stake are profound and represent a fundamental threat to our sovereignty. They should be a concern to all those who share democratic values," he said in reference to the terror threat faced by Britain.
"In defining as a terrorist anyone who opposes a brutal regime they alienate precisely that group that has to be onside if the extremists are to be defeated. We cannot be safe from the threats that emanate from that land unless the civil war is brought to an end," he added.
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