The director of BBC Scotland, Donalda MacKinnon, has said she wants to convince critics the corporation has no agenda, as a row about pro-union bias on Question Time escalated.

Speaking before the launch of a £32m dedicated television channel in Scotland, the cornerstone of the BBC’s efforts to address complaints from SNP politicians, TV companies and viewers that it has neglected Scottish audiences, MacKinnon acknowledged that “despite high consumption of BBC content in Scotland, higher than anywhere else in the UK, perceptions remain lower”.

Question Time became embroiled in fresh controversy after it emerged that a former Ukip council candidate who criticised the SNP during a broadcast from Motherwell two weeks ago was appearing on the programme for the fourth time. Amid further allegations that the SNP representative’s response to the man was cut, and that he had been personally invited to appear on the programme by production staff, MacKinnon denied this was the case.

She said: “It’s an absolute priority for us that audiences have confidence that we’re doing all we can to ensure fairness and balance in our news and current affairs output. I don’t want to talk about individuals but as far as Question Time is concerned there are robust procedures around audience selection and the production team does not invite people to participate.”

She said she had “full confidence” in Mentorn, the company that produces Question Time and will also produce Debate Night, the flagship current affairs debate series for the new channel, which launches next Sunday.

MacKinnon is well aware of the uphill challenge she faces in winning back viewers who lost confidence in the BBC during the independence referendum in 2014.

Acknowledging the anger some viewers felt about the corporation’s coverage of Scottish politics, she said: “I don’t imagine that we’re ever going to eliminate that, but the creation of an integrated nine o’clock news bulletin in the centre of the schedule, I hope, will go some way to addressing it.”

Pointing to research that found women with young children consistently value their news later in the evening, the new one-hour weeknight news programme – already notable for its diverse recruitment – will be warmer, less formal and “quite distinctive to anything we’re offering across the BBC,” she said.

Since taking up the post two years ago, MacKinnon and other senior colleagues have been noticeably more visible in public across Scotland. She said: “It is important for people to hear from us, and I blame myself that maybe we were too invisible [previously].”

Does she think it might it have made a difference in 2014, when protesters gathered outside the BBC’s Pacific Quay offices, if senior figures had been more proactive? “Yes undoubtedly I do, but that’s a dilemma that the BBC faces all the time, particularly when dealing with major political occasions like the independence referendum and fear of saying the wrong thing.

“But I am a firm believer, even in those who are very antagonistic towards us, to look them in the eye and try and persuade them there is no agenda.”

Ofcom has forecast the new channel will attract a small audience of 1.65-3.65% of Scottish viewers (the BBC has a 32% audience share overall) but MacKinnon said these numbers should be seen in the context the family of BBC digital channels.

“It is a challenging thing to do to launch a linear channel in a very busy marketplace with consumption habits changing rapidly and not just amongst the young, older audiences too. But for us its about content and making it live.”

The new channel was also an “opportunity to reflect the length and breadth of Scotland”, she said. It is notable that recent BBC traineeships offered Inverness and Aberdeen as a base as well as the Glasgow headquarters.

Last year, MacKinnon was tasked by the BBC director general, Tony Hall, with producing a set of recommendations for making the BBC “the best place to work for women” in the UK after the gender pay gap scandal. She delivered those recommendations last July.

She admitted that “there is cynicism that we’re an initiative-heavy organisation” but insisted the corporation was making significant progress. MacKinnon, who previously worked in a senior management role as a job-share when her three children were at school, pointed to the recently launched leadership development programme, progress in recruitment and flexible working policies.

She said: “But it’s an old organisation with a big history to it. Behaviour change is the big thing and once people see seismic shifts in the way people behave we’ll know we’re getting there.”