However, the highest-paid executive at the company was Director (Finance) A K Singhal, whose remuneration touched Rs 54.99 lakh in 2012-13 from Rs 46.26 lakh in the previous year.
Choudhury's total pay was Rs 53.87 lakh in the last financial year, a 53 per cent increase from Rs 35.15 lakh he received in 2011-12, according to NTPC's latest annual report.
His salary rose to Rs 30.03 lakh during 2012-13 period from Rs 15.99 lakh, while performance-linked incentives jumped more than 38 per cent to Rs 16.24 lakh from Rs 11.70 lakh.
Benefits accounted for Rs 7.6 lakh of Choudhury's total compensation package. He took over as CMD in September 2010.
Singhal, who has been Director (Finance) since 2005, received a salary of Rs 28.05 lakh, performance-linked incentives of Rs 11.75 lakh and benefits to the tune of Rs 15.18 lakh in 2012-13.
The company has not issued any stock options to its top executives in the past two financial years.
State-run NTPC, which has an installed power generation capacity of more than 41,000 MW, is the country's largest electricity producer.
The utility has projects with a generation capacity of about 3,555 MW under bidding, while feasibility reports for around 20,715 MW have been approved by the board.
NTPC's annual report has flagged various concerns of the power sector, including fuel availability and the financial health of electricity distribution utilities.
"In spite of various measures taken by the government, non-availability of coal and gas in desired quantity would have an adverse impact on the overall performance of the power sector," it noted.
According to the company, other concerns include difficulty in obtaining environmental approvals and land clearances.