I am not GST expert, still I try to give answer to your query on the basis of basic knowledge I acquired on GST.
Though there are many grey areas in some provisions in the GST, as far as salary is concern or the cost on employment is concern, there is no impact of GST, in general.
In case of supply of free goods or services to an employee exceeding the stipulated sum or if an employee avails of company asset for personal use say a car, a house etc., it would trigger GST.
The mechanism of input credit under GST i.e. input tax credit will not be available on supply of various facilities to employees, including life and health insurance.
You need to take expert advise on formulating CTC structure if it includes certain costs of facilities / fringe benefits.
From India, Mumbai
GST, which was under consideration and discussion since 1999, is expected to simplify the tax structure, create ease in logistics, increase the government tax revenue, and make tax evasion difficult. It is expected to have a huge impact on businesses of all scales.
GST does not cover income tax – and so does not have a direct bearing on salaried employees and organization's compensation and benefit programs, but it can affect certain parts of it. The perks, gifts, and subsidies – travel, food, and other subsidized amenities, given to employees which are not a part of their official CTC will be covered by GST. All the services provided by an employee to his employer which are within the scope of his employment contract will always be outside the ambit of GST and within the ambit of income tax. Services which are provided to the employer on principal to principal basis as an individual (i.e. part time Gym trainer services apart from normal employment services), could attract GST."