Yes. As per instructions given by TIN NSDL, a payer/ deductor need to use separate challans to deposit tax deducted under different sections of TDS. Payer also needs to indicate the correct nature of payment code in the relevant column in the challan 281. A dropdown is present while filing Challan 281 online. And a list of codes is mentioned at the back of challan 281 for offline payments.  

For example, A company made payment to contractor and rent and deducted TDS on both. Then here the company needs to use 2 separate challans. One for 194C for payment to contractors and sub-contractors, and one for 194I for rent.

However, from FY 2019-20 onwards, you can make the payment through a single challan for different nature of payments or different Section Codes in a month. CPC (TDS) has introduced a system where a single challan can be used for TDS payment under different section codes.