In the clip, Johnson tells a conference in Rome last week it was a "tragedy" that politicians in the region were "twisting and abusing religion" to advance their political objectives.
Such public criticism of British ally Saudi Arabia was seen by some commentators as a diplomatic blunder by Johnson, who has been on the job less than six months.
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"There are politicians who are twisting and abusing religion and different strains of the same religion in order to further their own political objectives," Johnson told the Med 2 conference.
"That's one of the biggest political problems in the whole region. And the tragedy for me — and that's why you have these proxy wars being fought the whole time in that area — is that there's not strong enough leadership in the countries themselves."
Johnson said there were "not enough big characters" willing to "reach out beyond their Sunni or Shia" group.
"That's why you've got the Saudis, Iran, everybody, moving in and puppeteering and playing proxy wars," he added.
Britain's foreign ministry stressed that Johnson had voiced support for Saudi Arabia on the BBC's Andrew Marr Show on Sunday.
"As the Foreign Secretary made very clear on Sunday, we are allies with Saudi Arabia and support them in their efforts to secure their borders and protect their people," a spokesman said.
"Any suggestion to the contrary is wrong and misinterpreting the facts."
Addressing a summit of the six-nation Gulf Cooperation Council (GCC) in Bahrain on Wednesday, May reaffirmed British support for traditional allies in the region and said Britain would help "push back against Iran's aggressive regional actions."
In a joint statement, the GCC states and Britain agreed to a "strategic partnership" and said they "oppose and will work together to counter Iran's destabilising activities".
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