The comments came as UK Prime Minister Theresa May ended a two-day tour of the Gulf, where she visited Saudi Arabia and lauded the UK's ties with its ally of 100 years.
"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 a conference in Rome last week.
"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 gaffe-prone foreign secretary has in previously hesitated when asked to condemn Saudi Arabia, particularly for its role in Yemen's ongoing war.
Under Johnson's watch, the UK Foreign Office has continued to defend arms sales to the oil-rich kingdom, despite accusations against Saudi Arabia of war crimes in Yemen.
Johnson himself went as far as to say in October that the controversial deals help maintain Britain's influence in the Middle East.
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As Johnson climbed political ranks, however, from being the mayor of London to unexpectedly landing the role as foreign secretary, his tone about Islam has become more conciliatory. |  |
Britain profits hugely from lucrative arms deals with Saudi Arabia, with the UK having approved £3.7 billion in arms contracts with the kingdom since it began bombing Yemen in March 2015.
The UK Foreign Office has attempted to to downplay Johnson's words, assuring reporters after his speech that the foreign secretary values and respects the UK's relationship with its key Middle East ally.
Although Johnson has criticised Saudi Arabia for its appropriation of religion - Islam in particular - the foreign secretary himself has in the past been sweepingly dismissive about British Muslims and scathing about the Islamic faith.
In an editorial written for the Spectator magazine in 2005, Johnson said that, "Islam is the problem," with regards to the problem of alienation faced by British Muslims.
He went on to describe Islamophobia as a natural reaction to reading the Muslim scripture, the Quran, saying that it is, "exactly what the text is intended to provoke".
As Johnson climbed political ranks, however, from being the mayor of London to unexpectedly landing the role as foreign secretary, his tone about Islam has become more conciliatory.
The same has occurred in his dealings with world leaders, where he has downplayed past gaffes and out of turn comments - most notably with Turkish President Recep Tayyip Erdogan, who Johnson penned a satirical limerick about prior to become the UK's top diplomat.
Johnson is set to visit the Gulf states at the end of this week, where he will probably soften his tone about Saudi Arabia and perhaps explain his comments.
