HRA

Dear Friend!

Take a note of the following:

Whether company can enter into an agreement with the employee, for HRA?

Kindly make your quesry more clear. Normally HRA is always part of the CTC of the employee under overlall offer letter or contract of employment and there is no seperate agreement for the HRA with the employees.

Employee is using the house owned by the company, can Er give HRA and later deduct from his salary under other deductions, inorder to avail sec 10(13a) benefits. 

Again quesry is not clear. HRA means "House Rent Allowance". So no employer will give first any allowance and later deduct the same under any deduction.

Will it make any difference for the company, if it gives RFA or HRA?

From employer's perspective it doesn't make any difference as whatever expense employer is incurring on his business operations, the same is tax deductible for him.