WHO estimates, 4.7 million people died in India as a result of the pandemic until last year, when hospitals ran out of oxygen and beds due to a record wave driven by the Delta variant.
India has reported only 524,002 COVID-19 deaths - the most after the United States and Brazil - with more than 43 million infections.
Actual infections are believed to be in the hundreds of millions in the country of 1.35 billion people. However, the Centre on Thursday rejected the WHO estimates saying the "validity and robustness of the models used and methodology of data collection are questionable".
It said in a statement, India has been consistently objecting to the methodology adopted by WHO to project excess mortality estimates based on mathematical models and despite objection to the process, methodology and outcome of this modelling exercise, WHO has released the excess mortality estimates without adequately addressing India's concerns.