The union has received a number of payslips from construction workers which show the deductions.
The apprentice levy was introduced last year and companies with a payroll of over £3m are expected to pay 0.5% of payroll costs to the HMRC for training.
Unite said: “Although highly immoral to pass this cost on to the worker, it is not illegal provided the worker has agreed to the deduction.
“In reality although workers will be unhappy about having the levy removed them their wages, most sign up in order not to lose the work they have been offered.”
But if an agency or umbrella company charges their entire workforce the apprentice levy they will be making an additional profit becuase they don’t pay the levy on their first £3m of payroll.
Unite assistant general secretary Gail Cartmail said: “The most unscrupulous umbrella companies and agencies are deliberately undermining the apprentice levy by forcing workers to pay something which is supposed to be their responsibility.
“In a double whammy not only are these companies offsetting what they should be paying they are potentially making a profit and lining their pockets through making deductions on the levy.
“The government must immediately look at this scam and introduce measures to prevent workers from being charged in this way.”