Kumar, who has been chargesheeted by the agency in a graft case, made the allegations in his letter to Delhi Chief Secretary seeking voluntary retirement.
CBI said making such "absolutely baseless allegations" after filing of charge sheet "is only an attempt to influence the matter which is subjudice".
"Central Bureau of Investigation strongly denies statement/news item published/telecast in certain sections of the media being attributed to Shri Rajender Kumar, IAS," CBI Spokesperson R K Gaur said.
Gaur said the accused had the opportunity to bring before the court any instance of alleged physical assault when they were produced before judge but no such allegation was made.
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"No such allegation was made at the relevant time, except one person, who also filed a writ petition in the Delhi High Court, but had to withdraw the same after the court observed that he is trying to spoil the system and scaring away the probe agency which was widely reported in the media on May 3, 2016," he said.
His reaction came after Kumar sought voluntary retirement alleging that he was repeatedly told by CBI interrogators to implicate Chief Minister Kejriwal.
In his letter to Delhi Chief Secretary, Kumar, a 1989 batch IAS officer, said, "I was repeatedly told that I would be let free if I implicate Chief Minister Arvind Kejriwal."
Gaur said the allegations of Kumar helping M/s Endeavour System Pvt Ltd (ESPL) in getting IT related contracts from various Delhi Government Departments, wherever he was posted, were in public domain since June, 2015 and were made by then Secretary, Delhi Dialogue Commission.
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CBI case is that while working in different capacities in Delhi Transco Ltd, Health and Family Welfare, GNCT, Delhi, Trade and Taxes Department and Delhi Jal Board from 2010-2014, Kumar had abused his official position to get contracts in favour of ESPL, a company which was managed by co-accused on his behalf, the official said in a statement.
"Investigation had established that the commission/bribe of around Rs.3.3 crores was also received by ESPL. During search, electronic items were found in the house of Rajendra Kumar, which were in fact purchased by ESPL for him," Gaur said.
When asked about Kumar's allegation against CBI, Union Minister Jitendra Singh said the Centre does not interfere in the functioning of the probe agency.
"CBI is independent agency and the government does not interfere in its functioning," said Singh, Minister of State for Personnel, Public Grievances and Pensions Ministry--which acts as nodal authority for the probe agency.
To a question on Kumar's reported move of seeking voluntary retirement from Indian Administrative Service (IAS), he said the government will see to it when such a request is received from the officer. Kumar is a 1989 batch IAS officer of Union territories cadre.