It says on the HRSDC website that if any temporary foreign workers have any complaints about their wages or work conditions, they should file a complaint with the Ministry of Labour of the Province they are working in. This would mean that the Czech pilots working in Toronto should file their complaints with the Ontario Ministry of Labour as indicated above.
However, I contacted the Ontario Ministry of Labour, and they indicated to me that because Airlines are Federally legislated companies, that any complaints that these particular Temporary Foreign Workers may have should be directed to the Federal Labour Ministry, not the provincial ones.