Yes, making late payments has a significant negative impact on the credit score. Your repayment history is the single largest factor in determining your credit score. Every late payment is reported by the lender to the bureau and reflects your payment behaviour. An individual with a high percentage of late payments is seen as having a high probability for payment default. This leads to a decrease in the credit score.
The single most important thing you can do to improve your credit score is to make all your loan and credit card repayments on time and in full.