IT contractors, oil and gas workers, locum doctors, social workers and nurses who took advice from accountants, recruitment firms and tax advisers face unexpected tax demands.
Mike Coupe, chief executive of supermarket chain Sainsbury's, says the UK needs to fundamentally review business taxes.
Personal finance reporter
A total of 700,000 people missed the deadline for submitting their self-assessment tax returns, according to HM Revenue and Customs.
This was little changed from the 746,000 who missed it a year ago.
More than 12 million people, many of whom are self-employed or have more than one source of income, are required to complete a tax return.
The deadline for paper returns for the 2017-18 financial year was in the autumn. The deadline for online returns was the end of 31 January.
The peak time for submitting was between 16:00 and 17:00 GMT on Thursday when 60,000 people filed.
Those who missed the deadline face a penalty of £100 during the first three months after the cut-off.
After three months, additional penalties of £10 per day can be demanded, up to a maximum of £900, followed by further charges six and 12 months after the deadline.