The restrictions were imposed on the Muslim Charity Run, organised by East London Mosque (ELM) and the London Muslim Centre, held earlier this month.
Communities secretary Steve Reed criticised the mosque’s decision to ban women from participating.
He said: “I saw these reports … and I was as horrified as anybody else.
“It’s absolutely unacceptable that women should be blocked from going on a fun run in a public space when the men are allowed to go out there and do that.
“We do not want a situation in this country where men are allowed to do things that women are then barred from. We cannot tolerate that.”
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The Muslim Women’s Network UK said while single-sex charity runs can be legally permissible, organisers could have taken “practical steps” such as different starting times or separate groups “to accommodate women and girls without compromising religious beliefs”.
The network’s chief executive, Baroness Shaista Gohir, said: “Such adjustments would have been straightforward and would have demonstrated a commitment to inclusion while avoiding the reinforcement of negative stereotypes about Muslims.”
The event attracted more than 1,600 participants, according to Tower Hamlets mayor Lutfur Rahman, despite the gender restrictions that limited participation to males of any age and females under 12.
He did not condemn the organisers when speaking to The Times.
He said: “What is important is that they have brought communities together – there is no room for criticism.
“There’s room for celebration and congratulating the fact that youngsters from a very young age to an elder who is 94 participated.”
Conservative councillor Peter Golds felt someone like Mr Rahman in public office “should be a little bit mindful about what they say“.
He added: “I do think it was strange that girls and women were omitted because it was in a public space and it was run by a charity.”
However The Standard yesterday quoted Mr Rahman as saying it was assumed women’s races were being held.
He added: “The council contacted East London Mosque to seek urgent clarification and the mosque have said in their statement that women’s races were not held at this event because of low take up but that they will organise women’s races going forward and work to increase women’s participation.
“Providing inclusive and accessible leisure and sport in Tower Hamlets and tackling barriers to women’s health and fitness, has been one of my top priorities.”
The Equality and Human Rights Commission is said to have launched an assessment of the case.
A spokesperson said: “We consider each [complaint] carefully and take action where appropriate.”
The East London Mosque defended its policy and believes it has been unfairly criticised.
A spokesperson said: “The suggestion that our event breaches the Equality Act is entirely incorrect.
“ELM encourages women to take part in sporting activities.
“There are many Muslim women from our community who have taken part in sporting events including boat races, cycling, hiking and marathons as well as various sporting challenges to raise funds for charity.
“We remain committed to listening to the needs of our community and ensuring our programmes serve everyone.”
Additional reporting by PA.
