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Southern Cleaning Services staff in Dunedin, employed by Broadbat, are concerned PAYE, KiwiSaver, student loan and child support payments deducted from their weekly pay may not have reached the Inland Revenue Department from their employer.
National MP Katherine Rich began investigations after receiving a call from a cleaner at Meridian Mall reporting the alleged anomalies.
Soon afterwards, calls from other Southern Cleaning Services employees started coming from sites in Dunedin, Roxburgh, Queenstown, Hamilton, Tauranga and Wairarapa.
She said she had received about 120 phone calls from past and present employees of the company, and had discovered some employees who believed their holiday pay had been underestimated.
"I think there are some disturbing discrepancies that need to be explained.
"Some of these people affected are heartbroken. They are really distressed."
When asked if Inland Revenue would investigate the allegations, spokesman David Balham declined to speak about the case specifically.
However, he did say the department would investigate any matters of "this nature".
"If an employer is taking an employee's tax payments and not passing them on, it's a serious matter."
However, Mrs Rich confirmed the Inland Revenue Department and the Department of Labour were investigating and were aware of the issue.
Mrs Rich said she had been liaising with IRD and the Labour Department and a freephone hotline (0800 473 566) had been set up to take calls from cleaners on the issue.
The line provides employees with advice on how to deal with the situation and those calling it have been asked to send their pay slips to the IRD so staff could discern what tax payments had been deducted and made.
Mr Balham assured affected employees they would not be penalised. "As long as they can show that the money has been deducted from their income, they have no further liability.
"They will not have to make any more tax payments. We would try to get those payments from the employer."
Attempts to contact Broadbat Ltd director Greg Thomas last night failed.