Is it permissible for an accountant to take a percentage from a travel agency for tickets he issues for his company, given that this percentage does not increase the price of the ticket?

It is not permissible for an employee to take a percentage from travel agencies offered to him, because gifts to employees are considered a bribe. However, it is permissible to take this percentage if the company you work for authorizes it, on the basis that the travel agency gave a discount to the company, and the company, in turn, granted you this discount.