Arvind Saxena, managing director of Volkswagen passenger cars, joined General Motors India as the president and managing director in February.
Sources said Chattopadhyay resigned at Volkswagen passenger cars India this week citing personal reasons.
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He had joined Volkswagen in 2012.
Chattopadhyay has spent two decades in the automotive sector. He has worked with Delhi-based Apollo Tyres and ExxonMobil.
Volkswagen has been under pressure in India for the past few years, with sales falling across segments.
Last financial year the company recorded a fall of 20 per cent in sales, much higher than the sector fall of six per cent.
Low volumes forced the company to pull out three models from India, Phaeton, Touareg and Beetle.
It has not introduced a model for many months.