A City of Cape Town councillor says the newly established Open Mosque has violated municipal by-laws by not having any parking spaces.
The mosque officially opened its doors on Friday despite criticism from members of the local Muslim community.
Founder Taj Hargey said the mosque would help counter radicalism.
“The City Council is trying to close the mosque using ridiculous bylaws and I will not be threatened by them or anyone else,” Hargey told the BBC.
“We have freedom of religion and expression in this country. No-one has the right to tell anyone what to believe in. This is a gender equal mosque, autonomous and independent and will remain so,” he said.
City councillor Ganief Hendricks denied that the closure request was part of a witch-hunt.
“This is an emotive issue – some councillors who are Muslim would want to defend the issue more vigorously than those that aren’t but the bottom line is we have to make sure that the rules are followed,” he told the BBC.
He said Hargey had not applied to change the use of the building from a warehouse to a mosque.
“There are issues of health and safety to consider before [a mosque] is set up,” Hendricks said.
A local by-law stipulates that a place of worship should have one parking bay per 10 worshippers on the premises but Mr Hendricks said there were not any.
The process of applying for the necessary paperwork could take up to six months, he said.
Hargey told the BBC that he believed everything was in order.
“It is pure intimidation. Why are they so scared? Because they know if this mosque succeeds their theological monopoly is over,” he said.
“This is not a gay mosque. But I will not turn anyone away based on race or sexual orientation.
“This mosque is based on the original mosque in Medina with one door where men and women come together to pray.
“I want my mother, wife, daughter to pray alongside me. Not be second class citizens. They pray together at Haj, why can’t they pray together in the mosques of the world?”