"There is a real danger that women entrepreneurs may be getting short changed in this tough investment climate," she said.
To correct the position ministers should launch an Investors in Women kitemark, and venture capitalists should monitor the gender of entrepreneurs backed, to help create sex equality in the new economy, says the report.
The prominence of female new economy icons such as Lastminute.com founder Martha Lane Fox masks underlying gender inequality in the sector, says the report.
Although the new economy, by valuing skills such as networking and team-building, promised to play to women's strengths, dot.coms have turned out to be as sexist as not.coms, Ms Wilkinson said.
"The huge potential for the new economy to transform the relationship between gender and wealth creation is not being realised," her report said.
She calls for measures such as a state-funded accreditation scheme for institutions which support female entrepreneurs, and women-led start-up incubators, to help promote equality.
"These initiatives are not simply a case of social justice or political correctness," Ms Wilkinson said.
"A new economy built on diverse foundation will be more creative and sustainable than one which simply reproduces the sexism of the old economy."
'Short changed'
Plummeting confidence in technology firms has further damaged prospects for female entrepreneurs by encouraging institutions to re-adopt conservative mindsets.
"There is a real danger that women entrepreneurs may be getting short changed in this tough investment climate," she said.
The venture capital firms which back start-ups remain dominated by "men in grey suits", many of whom are sceptical about the business acumen of female entrepreneurs.
"[They] often see women as consumers, targets for retail therapy online, rather than long-term business partners," Ms Wilkinson said.
The publication by institutions of gender-related statistics would help clarify discrimination, and help ensure the new economy does not miss an "historic opportunity".
"The talents of women are being neglected by the most vibrant part of the economy," the report said.
"Innovative, socially-aware approaches to business, many of them spearheaded by women, are being sidelined."
Ms Wilkinson launched business community site Elancentric.com, and Genderquake.com, an organisation committed to feminising the new economy.