Around 20,000 public sector workers are avoiding an average of more than £3,500 a year in income tax and National Insurance Contributions under the current system, according to the Government.
Sources claimed that an estimated 90% of earners who should comply with the rules do not.
Under the Chancellor's clampdown, state-backed organisations, instead of the individual, will become responsible for deciding if income should be taxed at source.
New guidelines will also be introduced to make it clearer when employment taxes should be paid.
MPs criticised the BBC in 2012 after it emerged 3,000 people were paid through personal services companies, potentially allowing them to limit their tax liabilities.