He said the commission has sought relevant data from income tax authorities in this regard.
Prime Minister Narendra Modi had on November 8 last year announced the scrapping of old Rs 500 and Rs 1,000 notes.
Citizens were provided a limited time window to deposit such notes in their bank accounts.
"We have already sought data (from the CBDT). We will get more refined data on which we will certainly proceed," Chowdary told PTI in an interview.
The CBDT or Central Board of Direct Taxes is the apex policy-making body for the I-T department.
Chowdary said he had had discussions with tax authorities on how to conduct the exercise as the number of transactions involving cash deposits for the country as a whole is very huge.
"So how do we see that whether the amount deposited by them (the employees) commensurates with their income or not.
Because the CBDT is already doing this exercise for everybody, irrespective of (whether) somebody is an employee or non- employee. We have taken the help of the CBDT. We are yet to get (data)," he said.
The CVC expects the CBDT to provide more specific data on the deposits. "We had a series of discussions with them as to what kind of analysis we would like them (to do). They are cooperating with us. In fact, they have given us a lot of ideas," Chowdary said.
He said the tax authorities suggested that the CVC take data in the actionable form.
Chowdary said the exercise being carried out by the CBDT requires writing of programmes, validating them and then generating right outcomes.
He said the CVC will look into the cases of central government employees and the staff of central public sector undertakings who are within the jurisdiction of the commission.
The anti-corruption watchdog has select categories of employees, usually Group A and B officers, under its jurisdiction.
"In respect of people who are not within the jurisdiction of commission, if the amount involved is beyond a threshold, we will send it to our Chief Vigilance Officers (who act as distant arm of the CVC) to take necessary action," Chowdary said.
Asked about the reasons behind the proposal to scrutinise the bank accounts of employees, he said there could have been some wrong deposits, but specific individuals and details of organisations they are working in may not be known now.
The CBDT is looking into certain suspected deposits made by various individuals, especially during the demonetisation period, Chowdary said.
Asked whether it would not be duplication of work, he said relevant data would be provided by the CBDT for the purpose.
"We are not duplicating. That is why we are getting refined data from the CBDT. That's why we said that you are anyway working on it ... That is why you share data of these (employees) people with us," Chowdary said.
In respect of individuals under its jurisdiction, the CVC also gets Suspected Transaction Reports (STRs) from the Financial Intelligence Unit (FIU).
The FIU is tasked with collecting, analysing and disseminating information related to financial transactions suspected to be involving black money or proceeds of crime.
An STR is a transaction of Rs 10 lakh and above believed to be involving proceeds of crime and black money.
In its report for 2016-17 released on August 30, the Reserve Bank of India (RBI) had said Rs 15.28 lakh crore or 99 per cent of the demonetised notes, had returned to the banking system.
The central bank in the annual report had said that only Rs 16,050 crore out of the Rs 15.44 lakh crore in the old, high-denomination notes had not returned.