Boris Johnson has accused Britain’s ally, Saudi Arabia, of engaging in “proxy wars” in the Middle East.
The Guardian newspaper has published footage in which the foreign secretary talks of politicians “twisting and abusing religion” for political gain.
He said Saudi Arabia and Iran were “puppeteering” because of a lack of strong leadership in the region.
The Foreign Office said Saudi Arabia was an ally and the UK supported its efforts to secure its borders.
In the footage from last week, Mr Johnson said: “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 is not strong enough leadership in the countries themselves.”
The foreign secretary told the Med 2 conference in Rome there was a lack of “big characters” in the Middle East who were willing to “reach out beyond their Sunni or Shia” group and bring people together.
He went on: “That’s why you’ve got the Saudis, Iran, everybody, moving in and puppeteering and playing proxy wars.”
The BBC’s diplomatic correspondent James Landale said the emergence of the comments would be “awkward if not embarrassing for the foreign secretary”.
“Once again Mr Johnson’s use of language is causing headlines that his diplomats will need to explain,” our correspondent said.
The video has emerged as Prime Minister Theresa May returns from a visit to the Gulf where she had dinner with the leaders of Saudi Arabia, Kuwait, the United Arab Emirates, Qatar, Bahrain and Oman.
A Foreign Office spokesman said: “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.”