The Foreign Secretary made the comments on a trip to Libya earlier this week, as he discussed how to stabilise the country following Western intervention and the fall of Colonel Gaddafi.
Hours after his words were reported, Mr Johnson risked a further row with the Prime Minister when he failed to back her position on student immigration data.
Speaking on his return to Britain, the Foreign Secretary told BBC Radio 4’s Today that the Prime Minister’s failure to secure a majority in June had highlighted the risk of calling an election too soon, and how it can serve to further undermine stability.
The Foreign Secretary was also repeatedly asked in the interview if he agreed with Ms May that the number of overseas students should be counted in net migration data, but failed to back her.
The interview followed the revelation that ministers may have based their policies on data that vastly overestimated the number of foreign students staying in the UK after studies.
Labour’s shadow Minister for the Cabinet Office Jon Trickett said: “The Foreign Secretary’s thinly veiled attack on the Prime Minister shows that there are deep divisions at the top of this Tory Government.”
Mr Johnson wrote in The Telegraph on Friday that unless Libya can reach a political union it risks becoming the “frontline” in the UK’s fight against terrorism and illegal immigration.
He underlined the country’s difficulties in The Telegraph, writing: “In Libya today there are three guns for every human – but there is no single source of law or authority, let alone power.
“There are two central banks, two rival parliaments, three prime ministers and up to four governments.”