"It is only a political motivation. There is no case... There is no truth," he told reporters after assuming office.
Earlier in the day, AICC General Secretary Ajay Maken sought Chowdary's resignation, citing bank documents that claimed that his company has defaulted on repayment of Rs 317.6 crore of loans with Central Bank of India.
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Asked about his vision for his ministry, Chowdary stressed on the need for focus in research.
"Everyone knows worldwide many of the inventions are done by Indians, but in foreign land. Instead of that we will work out foreign grants," he added.
"More incubation centres can be encouraged to be set up in universities across the country," Chowdary, who holds a post graduate in engineering, said.