Scotland’s health secretary has reported a nursery to watchdogs, alleging that his daughter was refused a place because she is not white.

Humza Yousaf said the Little Scholars Nursery in Broughty Ferry, Dundee, told him and his wife that there was no place available for two-year-old Amal.

But he said applications submitted by friends and family using “white Scottish-sounding names” were accepted, prompting him to ask the Care Inspectorate to investigate.

Mr Yousaf said the evidence gathered by he and his wife “proves our case beyond doubt” and added: “We are fooling ourselves if we believe discrimination doesn’t exist in Scotland.”

The nursery denied the allegations on Monday, stating they were “demonstrably false” and noting that its owners were of “Asian heritage”. It “absolutely” welcomed the inquiry and said “we have nothing to hide”.

However, Mr Yousaf tweeted that the nursery had been given “every opportunity” to provide an explanation for the “disparity in treatment” and “none has been forthcoming”. He and his wife, Nadia El-Nakla, are also seeking legal advice.

Ms El-Nakla emailed nursery bosses in May asking for a place but she was informed there were “no available spaces”, the second time the couple said their application had been rejected.

But they claimed that when a white friend asked if there was a space for her two-year-old son only two days later, the nursery offered a place on three afternoons a week.

The Daily Record then submitted applications with identical requirements to the nursery under the names Aqsa Akhtar and Susan Blake. The newspaper said Aksa Akhtar had her application rejected, but Blake’s was accepted and offered a space.

In a series of tweets, Mr Yousaf said he had initially rejected suspicions that the rejection of his daughter’s application was “Islamaphobic or racist” but his wife’s “gut instinct” was that “something just wasn’t right”.

He said he would “love for there to be another explanation for all of this” but the nursery’s reference to its Asian owners was “effectively the ‘I can’t be racist, my pal is black’ defence. That doesn’t fly any more”.

Mr Yousaf tweeted: “It doesn’t matter what my position or how senior in Govt I may be, some will always see me, my wife [and] children by our ethnicity or religion first.”

He concluded: “With no explanation from Little Scholars, we will pursue the truth [and] get answers we deserve.”

Douglas Ross, the Scottish Tory leader and a father of two young children, tweeted: “This is an awful situation and no family or child should suffer discrimination because of their name and background. This should be investigated and stamped out.”

A spokesman for the nursery said: “Our nursery is extremely proud of being open and inclusive to all and any claim to the contrary is demonstrably false and an accusation that we would refute in the strongest possible terms.

“In addition to our owners being of Asian heritage, across more than a decade we have regularly welcomed both children and staff from a range of different religious, cultural, ethnic and racial backgrounds, including two Muslim families currently.”

The nursery said it regularly provided a halal menu for Muslim children and it looked forward to demonstrating “the policies and procedures we have in place to ensure we are a nursery that is open and welcoming to all”.