Generally when you are taking services from other company, whether on contractual basis then you have made some agreement and in which you have made payment terms which are subject to applicable TDS or not. If the agreement is silent about it then you will pay the amount of tax as mutual consent with parties, like you can do barter deal etc to escape the tax.
If the contract of service is mentioning the TDS provisions then you will make payment to naukari.com on deduction of tax as per section 194C of the Income Tax Act, 1961.