In a statement of claim expected to be lodged with the Federal Court this week, United Voice alleges Phillips Cleaning Services signed up S'gaw Karen refugees from Myanmar and Thailand with limited or no English to contracts they did not understand. The union claims workers were regularly moved between business entities with different names and business numbers without adequately explaining why or informing the ACT government. Fairfax has sighted payslips that show one worker being paid by four businesses with similar names but different ABNs. The union has also named Rose Cleaning Service in a complaint to Ms Burch.

The union's statement claims some workers are owed as much as $24,751 in lost wages – a claim strenuously denied by spokesman Sam Cassaniti acting for both companies.

The two companies are contracted to clean about 19 ACT public schools in Canberra from Belconnen to Tuggeranong.

One of the cleaners, Htoo Ywai, who came to Australia as a refugee from Thailand and spent more than 20 years in a refugee camp with his mother and family, said he was never paid extra for doing the work of other cleaners when they were away.

Speaking through a family interpreter, he said he worked regularly with chemicals but had not been given gloves or safety masks, despite asking for them.

A statement prepared for the cleaning companies said the dispute stemmed from a refusal to enter into a proposed enterprise agreement promoted by the union. The statement said the union threatened to bring about a payroll tax audit if they continued to refuse to sign the agreement.

Mr Cassaniti said the union was claiming the cleaners were entitled to be paid when not working during school holidays, which was not in the contracts, and most of the workers did not want to work over these times.

"[The cleaning companies] strongly maintain that they are exemplary employers. There is no dispute by any of the cleaning service providers that workers should be paid a good wage, and one in step with the rates clients (including the Department of Education) are, themselves, prepared to pay for cleaning services. Indeed this is happening," the companies said.

In a letter to Ms Burch, United Voice ACT branch secretary Lyndal Ryan also claimed Phillips Cleaning failed to pay the correct wages to one union member for two years, failed to supply the level of labour the company was contracted for on several occasions and in one instance, directed a cleaner to forge his director's signature on a time sheet to make it appear that the contracted level of labor had been supplied – claims refuted by Mr Cassaniti.

Ms Burch said she had instructed the education and training directorate to investigate the claims, and external agencies had been engaged.

"The examination of these matters is ongoing. It is an absolute priority of the government that we ensure the safety and working conditions of contract cleaners and I am committed to getting to the bottom of these allegations," Ms Burch said.

A safety report commissioned by the union into conditions at Alfred Deakin High School, cleaned by Phillips, raised concerns about inappropriate storage of chemicals, electrical safety and inadequate protection equipment, concluding, "The fact that so many instances were found where workers were exposed to hazards and suitable hazard controls were not in place or monitored suggests a serious incident is inevitable unless significant improvements are made".

Mr Cassaniti said the only safety issue that had occurred had been one cleaner bringing bleach to work in an incorrect container, and this had been appropriately dealt with by the employer.

A Department of Education and Training spokesman said he could not comment on the specific allegations raised by United Voice, but to date the directorate had found no evidence to warrant contracts being discontinued.