The party said it had asked Arthur Thackeray to engage with Nil By Mouth on the back of the bigotry row.
He had also said Catholicism was based on fascist ideology and complained of a "suffocating culture of anti-loyalism" in Glasgow.
In another move, the party's lesbian, gay, bisexual and transgender (LGBT) section said Mr Thackeray should "reconsider his role and membership within Ukip" if he was opposed to gay people as a section of the population.
Nil By Mouth said it was giving the request "due consideration".
The move follows Ukip's decision to suspend Henley-on-Thames councillor David Silvester, who claimed that recent floods were the result of the UK Government's decision to legalise gay marriage.
Ukip Scotland head of policy Jonathan Stanley said: "While everyone has a right to express their views my belief is that the chance should be taken to distance Ukip from comments that are not supported by the party.
"As head of policy I have to ensure we credibly deliver a non-sectarian approach in supporting the United Kingdom in Scotland."
Ukip LGBT's Thomas Broker added: "Mr Thackeray's views are not in line with the Party view. Given his position we ask him to withdraw his remarks and apologise.
"It is bewildering to hear that 'gays' are behind the anti-unionist movement, and if Mr Thackeray sees gay people as an opposition or a movement to which he is opposed, he should reconsider his role and membership within Ukip.
"By engaging with people more closely in society, Mr Thackeray will learn that British Unionism and UK independence has far reaching support from people of all demographics."
Mr Thackeray, who works in the security industry in Glasgow, became acting chairman on the back of a disastrous period for the party in Scotland.
Key figures quit their posts recently, while Scottish leader Lord Monckton was fired in a bitter civil war.
At the weekend the Sunday Herald revealed some of Mr Thackeray's views on religion, including a 2011 post where he stated: "There's more chance of winning the lottery two weeks running than getting an openly Rangers-supporting MSP into the chamber of the institutionally catholicised pretendy parliament ... lol."
He also criticised Glasgow City Council, stating: "No wonder the blue half of my city say GCC actually stands for the Glasgow Celtic Council for gays Catholics Communists eh. Lol. NS!"
In a letter to Nil By Mouth, Mr Stanley adds: "We are aware of the long standing sectarian divide that has affected many in Scotland and support the overwhelming majority of Scots that do not support comments that are sectarian in nature.
"Ukip supports your charity's work in reducing tensions in communities through various community projects.
"I have asked the chairman, Arthur Thackeray, to engage with your Beyond Religion and Belief project to ensure that in support of the United Kingdom that Ukip will first and foremost be a party of local democracy and communities."
One Ukip source said: "The party around Glasgow has a lot of people into the whole football thing. For them its really a party of British Unionism, not an anti-European Union party."
A Nil by Mouth spokesman said: "We've received a request from Ukip in London for its Scottish branch to engage with our sectarianism awareness programme.
"We will give this request due consideration should the Scottish branch follow up this contact."
Mr Thackeray was unavailable for comment.