A Whitehall official who ran the scheme that granted Jennifer Arcuri a coveted entrepreneur visa had worked for Boris Johnson when he was mayor, the Guardian has learned.

The US businesswoman, who is at the centre of a conflict of interest row over her friendship with the prime minister, beat nearly 2,000 applicants to gain one of 200 sought-after tier 1 entrepreneur visas on the government’s Sirius programme after Johnson helped promote her firm, Innotech, by giving keynote speeches at her events.

The Guardian has learned that Paola Cuneo, the then director of the Sirius programme, previously spent two-and-a-half years working in a senior post at London & Partners (L&P), the official mayoral promotional agency which Johnson had responsibility for while he was in City Hall.

Cuneo, Arcuri and Johnson attended the same Innotech event in October 2013, two months before the company joined the Sirius scheme.

Facebook Twitter Pinterest Boris Johnson at the event in 2013 with Arcuri (left) and Cuneo (far right, back to camera). Photograph: Twitter

A whistleblower told the Guardian: “Innotech stood out compared to other startups in the programme, which had a much higher potential to scale up … I could not understand why we were giving so much attention and extra funds to Innotech.”

Ten days after the news of Johnson’s relationship with Arcuri broke, the new disclosures will intensify speculation over a possible conflict of interest and raise fresh questions for the prime minister over whether he played an improper role in securing government support for his friend. Johnson has insisted that “everything was done with full propriety” but repeatedly refused to go into detail on what help, if any, he gave to Arcuri.

On Tuesday, Johnson refused three times to deny outright that he had an affair with Arcuri in an interview with Sky News. When pressed on whether he was denying an affair, he said: “The crucial thing is that in terms of promoting London, everything was done with complete propriety.”

The latest twist follows revelations that firms run by the entrepreneur – who is said to have confided in friends she was having an affair with Johnson – received £126,000 of public money. About £11,500 of that figure was paid by L&P to Innotech while Johnson was mayor and after Cuneo left the agency. Arcuri also went on three overseas trade missions led by Johnson, two of which she had initially been turned down for.

The Sirius scheme, run by UK Trade and Investment (now the Department for International Trade), aimed to attract international entrepreneurs to set up businesses in Britain by providing visas, expert advice and mentorship, as well as a £12,000 grant.

According to evidence provided to the Guardian by a whistleblower, staff working on the Sirius programme warned Cuneo and other senior civil servants of a conflict of interest in June 2014 after Innotech was given £10,000 by the scheme to run a launch event for the programme the month before before without any tendering process.

Staff were concerned that the programme team failed to follow procurement rules and warned there was a conflict of interest with the Sirius scheme paying the startup because it was already a recipient of the visa scheme.

Speaking this week, the whistleblower accused Cuneo of showing favouritism towards Innotech and questioned the company’s suitability for a place on the programme given it was simply an events firm rather than developing a product.

The whistleblower, who worked on the Sirius scheme at the time, told the Guardian: “I regarded the two decisions about Innotech [on the visa and the subsequent launch event contract] as examples of favouritism.”

Innotech was the only company admitted in the first wave of Sirius startups that did not have a tech product, the whistleblower said.

“It was fundamentally an event company. In that sense, Innotech stood out compared to other startups in the programme, which had a much higher potential to scale up. Potential to scale was one of the criteria we adopted to evaluate applicants.

“This is significant because admission to the Sirius programme involved a tier 1 entrepreneur visa, plus a grant of £12,000, plus additional support resources.”

The whistleblower said that after Innotech was admitted, Cuneo decided to give the firm an extra £10,000 to organise a launch event for the Sirius programme.

“Several members of the team raised concerns about that decision, because it seemed not to follow standard procurement rules and because there was a clear conflict of interest (as we had already funded this startup). There were concerns because those services were procured without opening up the tender to competition and because the invoicing seemed to be irregular. On top of that, we already had a supplier for event management, so this seemed like a duplication.”

Facebook Twitter Pinterest Arcuri and Cuneo at the Innotech Sirius programme launch. Photograph: Paul Clarke

Cuneo was the director of the Sirius programme from May 2013 until August 2016, boasting on Linkedin that she “designed, launched and ran the programme from its inception including business cases approval, suppliers and stakeholders management, team leadership”. The profile describes her role on the programme judging panel “reviewing a number of global applications for their assessment against key criteria as part of the panel of judges”.

Prior to that, she served as head of L&P for Europe, the Middle East, Africa and Asia and Pacific from 2009-11 while Johnson was mayor in City Hall where he served from 2008-16.

Cuneo attended at least two Innotech events in 2014, including one at the House of Commons. In an Innotech promotional video recorded after she spoke at a joint Sirius/Innotech event, she said: “I think today was amazing, so inspiring. It was great to have representation from the VC world, the corporate world, the startups, the accelerators.

“We’ve gone out of our way all over the world [to] select the best talents and we put them into the UK, which as we’ve heard today is a pretty amazing place to be an entrepreneur.”

She also sent a number of supportive tweets about Arcuri, writing to her in October 2015 saying: “You nailed it.” More recently, in 2016, Cuneo wrote that she was “very proud” of Arcuri.

The whistleblower added: “Before leading the Sirius programme, Cuneo was holding a senior position at London & Partners. At that time, I could not understand why we were giving so much attention and extra funds to Innotech – in light of the news that has been published last week, I started to make a possible connection. That is why I came out with this information, which I believe to be of public interest.”

The Department for International Trade declined to comment. Arcuri and Cuneo did not respond to requests for comment.