Boris Johnson told a conference in Rome last week it was a "tragedy" that politicians in the Middle East were "twisting and abusing religion" and said Saudi Arabia and Iran were "puppeteering".
Such public criticism of British ally Saudi Arabia was seen by some commentators as a diplomatic blunder by Johnson, who has been in the job less than six months.
"Those are the foreign secretary's views. These are not the government's position on, for example, Saudi Arabia and its position in the region," Prime Minister Theresa May's spokeswoman said, adding that she has "has full confidence" in Johnson.
The comments were made public at an embarrassing time as May had pledged to strengthen ties with Gulf states including Saudi Arabia at a summit in Bahrain earlier this week.
In a video posted on the Guardian's website, Johnson told the Med 2 conference: "There are politicians who are twisting and abusing religion and different strains of the same religion in order to further their own political objectives.
"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."
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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.
The foreign ministry stressed that Johnson had voiced support for Saudi Arabia in a BBC show on 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, GCC states and Britain agreed to a "strategic partnership" and said they "oppose and will work together to counter Iran's destabilising activities".