Self-employed women earned 40% less than self-employed men in 2012, according to the figures published by HM Revenue & Customs. Its Personal Income Statistics 2011-12 report shows that, while average income for a self-employed man was £17,000, the equivalent for women was just £9,800.

The gap is widest in London, where women earned less than half the £25,700 average income of a self-employed man. Next came the east of England and the east Midlands. In almost every region apart from London, the south-east and Scotland, self-employed women earned less than £10,000 a year, the report reveals.

The revelations follow research by the Office for National Statistics (ONS), which showed that the gender pay gap in the UK widened for the first time in five years in 2012, from 9.5% to 10%. It found that women have made up more than half the 10% growth in self-employment since the recession began.

Some economists have speculated that many people who register as self-employed may have done so after failing to secure employment, because the rise in self-employed individuals, to almost 4.4 million, has coincided with a fall in employee numbers.

Frances O'Grady, general secretary of the TUC, said: "There may be perfectly good reasons for being self-employed, but it would be naive to think that all these workers are really budding entrepreneurs."

She added: "These figures instead suggest that many employee roles are being replaced by self-employed positions. Bogus self-employment is bad news for workers because they miss out on vital rights at work – such as paid holidays and employer pension contributions – without having the advantage of being their own boss."

The Women's Budget Group, a campaign organisation, noted in a recent report that "much of this increase [in women becoming self-employed] was effectively in precarious work or zero-hours contracts, rather than the creation of new businesses."

Scarlet Harris, spokesman for the group, said: "Clerical, cleaning and caring work, which is predominantly carried out by women, has experienced some of the fastest growth in self-employment in recent years. These women, who already suffer poverty rates of pay, are now having to contend with the poor working conditions and complete lack of job security that self-employment brings. These shocking gender pay gap figures should end any delusions people have about the UK's four million self-employed workers."

Evidence has emerged that the government encourages benefit claimants to register as self-employed, so as to remove them from official employment statistics. A BBC investigation last month found that advisers exhort individuals on the welfare-to-work scheme to become self-employed, in order to shift them from unemployment benefits to working tax credits.

Self-employment also tends to negatively affect an individual's personal finances. Debt charity StepChange has warned that the self-employed are, on average, burdened with four times the debt of employed workers.

A conference entitled Women's Assembly Against Austerity convened last month, following a report revealing that low-income women have been worst-hit by austerity measures and the economic downturn.