Johnson accused the two countries for sparking proxy wars in the Middle East and abusing Islam as a tool to do so, while speaking at a conference in Rome last week.
"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 said.
"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," he added.
His comments break a long-established Foreign Office convention that prevents government ministers from criticizing UK's allies publicly.
Britain has had a long alliance with Saudi Arabia, relying heavily on exports to the kingdom.
The region hosts a number of key British military bases as well.
The kingdom recently announced its plans to issue five-year multiple entry visas for British business people, facilitating the process for trade between the two.
The news comes just days after UK's Prime Minister Theresa May returned from a visit to the Gulf.
May urged Gulf leaders to "follow through with social and economics reforms in her speech at a summit in Bahrain," according to The Guardian.
According to May, the UK's influence in the region is only possible "because the strength of the relationship between our countries, and the respect that we have for each other, enables us to speak frankly and honestly as friends."