Some NGO's might be covered by the Shops & Estbs Act.
So you can approach:
Inspector appointed under Shops & Estbs Act if the establishment is covered by the Act and you are covered by the def. of 'Employee' in the Act
O/o Labor Commissioner; if you are covered by the def. of 'Workman' as in ID Act
Inspector appointed under Payment of Wages act if your wages are within the def. of wages in the Act
Take help of employee's/trade unions, a very able counsel specializing in Labor/service matters...