The number of verified refunds pending as on November 29 are 20.76 lakh and currently being processed.
Chowdary was in August 2014 appointed as chairman of the CBDT, the top policy making body of the income tax department.
The scheme is being implemented in a hurry without considering the concerns of the majority of the stakeholders, said the letter.
The number such individuals having taxable income of over Rs 1 crore stood at 81,344 during AY 2017-18.
The section does not provide any timeline for companies to opt for the new regime of lower tax rate.
The CBDT, which frames policy for the Income Tax Department, issued a circular on Thursday stating exceptions to the new system.
In order to avail the facility a taxpayer will have to file an application for compounding a tax offence before the competent authority.
Out of the 5.65 crore ITRs filed so far, 3.61 crore have been verified.
If a person has already withdrawn Rs 1 cr or more in current fiscal, the 2 pc TDS shall apply on all subsequent cash withdrawals.
FM on Friday announced the withdrawal of enhanced surcharge on short-term and long-term capital gains earned by FPIs.