Supply of food in Canteen by the employer to employee is covered under the definition of supply. [Sec 7(1)(a) of the CGST Act]
The Canteen facility is a business activity carried by the co. ancillary to its main business activity i.e. manufacturing. [being taxable under Schedule II Clause 6 of CGST Act]
Cost recovered from the employees is covered under the term consideration. [under Section 2 (31)]
Hence, the recovery of expenses/cost per meal from employees is taxable under GST.