Tom Macartney threw out applications for operating licences from Pentland Commercials and B Kennedy Commercials after raising concerns about the two women behind the companies.
He also expressed worries about a "significant overlap" between the two firms, which were intending to use the same premises in Dunfermline.
Commenting on Laura Powell, who claimed to be sole director of Pentland Commercials, the commissioner said:
"Miss Powell displayed a level of ignorance which, had she been a genuine sole director, would doom this haulage firm to failure."
And of Darlene Bell, a director of B Kennedy Commercials who had worked alongside Miss Powell as a social care worker for East Lothian Council, he added: "She did not have a transport manager and did not have experience in running transport herself."
The commissioner published his ruling yesterday following public inquiries held in Edinburgh on 2 March.