Of the 58 approved entries for the Scottish Edge awards, 28 were linked to Entrepreneurial Spark, or ESpark, whose chief executive Jim Duffy helped judge the applications.
It is the second time the publicly funded scheme has had Duffy on the panel, an inclusion which budding entrepreneurs have branded a "conflict of interest".
Run by Scottish Enterprise on behalf of the SNP Government, the Edge is a Dragons' Den-style competition for aspiring wealth creators.
As revealed by the Sunday Herald, £704,000 was shared out between 18 businesses in "round two" of the scheme in June.
Over half of the 30 finalists were under the wing of ESpark, a social enterprise that nurtures new businesses, as were 16 of the 18 winners.
Duffy, who earns around £90,000 a year as ESpark CEO, did not sit on the final judging panel in round two, but he was a member of the team that selected the finalists.
Nearly 90% of the £704,000 prize money went to ESpark "chiclets" - the name given to businesses under its wing.
A similar pattern has now emerged in round three, where £775,000 is up for grabs. Duffy and the other judges recently whittled the 301 applications down to 58 businesses, which will compete at a semi-final event tomorrow. According to Scottish Enterprise, 28 of the 58 ventures are linked to ESpark.
Duffy has continued as a panellist, despite nearly 10 individual concerns being raised with the quango about his presence in round two.
The concerns prompted Scottish Enterprise to meet the Government to address the issue, and a section on "impartiality" was put on the quango's website. However, Duffy was allowed to stay on for round three.
The blurb stated: "Many Scottish Edge applicants may have a working relationship with one or more of the organisations who enable and support businesses starting up in Scotland. It is therefore inevitable that some judges may be more familiar with a particular applicant than others.
"No single judge's assessment would be sufficient to artificially skew the overall conclusions and applicants are assured that their selection, or otherwise, is undertaken in a professional and consistent manner."
However, Duffy's presence has angered some of the unsuccessful applicants. Chris Gillan, whose Heroes Drinks Company Ltd did not make the round three semi-final, has called for the Edge Awards to be "put on hold pending a review".
He said of Duffy's involvement: "This has made a complete mockery of the competition and without a shadow of doubt is a conflict of interest. Mr Duffy's position on the panel of judges is unethical."
Saul Page, whose Go Army venture also did not make the cut, told the Sunday Herald: "I feel that John Swinney and the SNP should have ensured fairness and transparency to the judgment and panel of the competition. Mr Duffy being on the initial panel is a conflict of interest which is clear by the percentages of the public funds being awarded to Entrepreneurial Spark companies.
Eleanor Mitchell, commercialisation director at Scottish Enterprise said: "Almost all of the applicants have connections with one or more of the organisations involved in the judging process, but to suggest any one single judge has the ability to influence conclusions of the panel is incorrect. Each applicant is assessed purely on the information submitted and judging has and continues to be undertaken on an equal basis without partiality."
SNP MSP John Wilson said: "It is clear the conflict of interest still exists. It is also disappointing Jim Duffy was allowed to continue as a panellist in round three after concerns were raised with Scottish Enterprise."
ESpark did not respond to a request for comment.