Travelling Per diem

If included in employment contract It would've been escaped the GST liability since it would be called a service in the course or in relation to the employment and consequently attracts Schedule III provisions..

In your case it would be taxable as per provisions contained under Schedule I (para 2) because It would be treated as perquisite (free gift). But It's taxable only if the valuation per employee per annum is exceeding ₹50,000...

As per the press release dated 10/7/2017 issued by CBIC , The services provided employer to employees in the course of or in relation to his employment outside the scope of GST.

Hence transaction between Employer & Employee is excluded from levy of GST if :
1. In relation to employment.(Schedule III)
2. Gift not exceeding 50K (Schedule I)