Johnson compared women wearing the veil with bank robbers or letter boxes in an article for the right-leaning Daily Telegraph.
The Conservative MP will face an investigatory panel for a possible breach of his party's code of conduct, the first step in disciplinary action that has been called for by a number of Conservative MPs and independent organisations.
Johnson left May's cabinet in July in a dispute over her plan for leaving the European Union, which he says he finds too soft.The comments prompted severe criticism from within his own party, including Prime Minister Theresa May, and led to questions about whether he was pandering to the far right by stoking Islamophobia.
He is considered a frontrunner to replace May should she resign, and has support among Conservative supporters to the right of the prime minister.
Johnson is reported to have recently secretly met US far-right ideologue Steve Bannon, a former adviser to US President Donald Trump.
Bannon has come out in support of the MP, saying in July that "now is the moment" for Johnson to challenge May.
If found to have broken the Conservatives' code of conduct, he could face expulsion from the party.
A hundred Muslim women who wear the niqab had written to Brandon Lewis, the chairman of the Conservative Party, demanding that Johnson be kicked out of the party.
"Our decision to wear the niqab or burka is not an easy one, especially given the hate that many of us experience on a regular basis. Nevertheless we do so because we believe it is a means to get closer to God," the women said in a letter.
Lewis and Theresa May have both criticised Johnson for his remarks and have urged him to apologise but he has so far refused to do so.
The Muslim Council of Britain (MCB) has welcomed the party's decision to launch an inquiry into the former foreign secretary's comments, a statement published on Thursday said.
"While the choice of panelists are for the Party to decide, to avoid accusations of a whitewash, the group should include people who are aware of the seriousness of the issue and its effect on society," Harun Khan, secretary general of the MCB said.