The Home Office has suspended a passport official and ordered a disciplinary investigation after the employee subjected a gay father-of-two to a lengthy interrogation about his sexual history and the details of his adoptions in front of the man's four-year-old son.

During what was meant to be a routine interview – the final stage in the application for his passport – Randall Cole was last month questioned for half an hour about his sexual practices, including whether he had ever had sex with a woman, and forced to discuss the terms of the adoptions and his relationship with the biological mother. He was also asked whether his children were "confused" by their family – as the child sat on his lap.

Cole says the "clearly homophobic" questioning left him shaking and feeling "violated and dirty" and wondering, amid the widespread delays with 400,000 people waiting for their passport, whether the system is "so broken that it allows people to do and say whatever they want without fear of repercussion".

Randall Cole, who became a British citizen this year.

American-born Cole, 44, a charity worker who became a British citizen on 1 May and who married British human resources manager Stuart Wales, 42, in California in 2001, went to the passport office in Chelmsford, Essex, expecting a "straightforward interview".

The Home Office website states that applicants will simply "be asked to confirm facts about yourself that someone trying to steal your identity may not know".

But in the midst of an open plan office, the official then "launched immediately into personal things".

"I told her I am here with my son Samuel and that he has an older brother [Benjamin, eight] but that my husband is looking after him – and when I used the term husband that's when you could see something immediately changed in her. She began to fixate on questions about my family.

"She said: 'Is this your biological child?' And when I said no she said: 'Is it your partner's biological child?' And when I explained that we are family through adoption she said: 'Oh, so that's why you're able to have children.'" Cole tried to distract his son with a box of Tic Tacs.

"She then asked 'What do the children call their birth mother?' and 'What does the birth mother think about all of us?' and 'Aren't the children confused by it all?'"

Cole attempted to explain that if Samuel's birth mother was there and the boy fell over he would run to Cole. But the officer "sighed, shook her head and looked bemused".

"Then she said: 'What do you think people make of you when they see you walking down the street with your kids?'"

The official, he says, went on to ask about the birth mother: "Do they call her mum? Why didn't she want to keep her children?" Concerned about the effect of this on his son, Cole felt compelled to again explain things to him, in front of her.

"I'm talking to Samuel, even though he knows this, saying: 'You came out of Emily's tummy but Daddy and Papa are your parents.' At this point I felt I was failing my son, failing to keep him safe," he says.

When Cole mentioned that he works part-time, he says, the Home Office employee interrupted: "Oh, so you're like the housewife." The grilling reached another nadir, however, when matters moved on to Cole's sexual history.

"She said: 'You must have had relationships with women in the past though?'" At this, Cole stopped her.

"She became indignant and said: 'We can ask anything we want, regardless of whether or not it makes you feel uncomfortable.'

"But it was clear she was trying to humiliate me – a way to get me to say if I'd had sex with a woman. She said I could refuse to answer but my lack of response would be noted and then proceeded to try to get me to answer, through a variety of questions, whether I or Stuart had previously been sexually active heterosexually." He has filed a written complaint to the Home Office.

"I have never felt so violated or humiliated. Her questioning was clearly homophobic, designed to put me in my place. We moved here because of the promise of a tolerant society."

Such Home Office interviews are recorded as a matter of routine. It is understood that the recording has been reviewed by more senior Home Office officials.

A Home Office spokesman said: "Intrusive questions about someone's sexuality as part of an interview would be inappropriate and is not a reflection of our policy.

"The member of staff in question has been suspended and a disciplinary investigation is now under way."