CVC Pradeep Kumar and CBI Director A P Singh are understood to have raised concerns over the present form of the proposed anti-corruption bill and sought its redressal.
Sources privy to the development said that Kumar had objected to the proposed inclusion of 'Group C' employees comprising clerical staff under the CVC ambit.
"The CVC directly advises action in vigilance matters related to Group A and B employees. Whereas, it supervises the proceedings by concerned departments in matters related to employees under Group C and D.
"The group C employees are under overall supervision of the commission. The proposals to have their direct control will require more manpower and official resources. The commission in its present form may have difficulty in dealing with it," a source said.
Kumar is understood to have proposed to the prime minister widening the scope of the commission's work.
Sources said there may be a conflict of interest between the CVC and Lokpal as both will have powers to probe any complaints of corruption involving central government officials including those working in banks and public sectors.
"There has to be a proper division of work between the CVC and the Lokpal. The powers of two bodies should not be made contradictory to hamper probe in corruption cases," the official said.
Whereas the country's premier investigating agency has expressed unhappiness over many issues related to the Lokpal, saying many of the clauses would severely impair the functioning of the investigating agency.
In its letter to the department of personnel and training, the CBI said the proposed move to make preliminary inquiry by Lokpal mandatory before giving cases to CBI will "severely impair" effectiveness of the agency in anti-corruption cases as it would lose the "surprise element" to carry out search operations.
Sources said the CBI director raised the matter with the prime minister during their meeting.
According to the letter, the agency at present gathers information from various sources and plans and executes a search operation to collect documents and evidence. But if the preliminary inquiry by Lokpal is made compulsory and if the suggestions would be implemented, the agency will lose the "surprise element" to carry out such operations.
The agency also cited lack of enthusiasm about the recommendations of the Parliamentary Standing Committee on Lokpal Bill that all complaints of corruption cases which are in the nature other than trap cases shall first be scrutinized by Lokpal by holding a preliminary inquiry.
The CBI also made a strong pitch for ensuring that its legal authority and operational effectiveness are not diluted when the proposed Lokpal becomes a reality.
Sources said Dr Singh has listened to the heads of the CVC and CBI and assured to resolve their concerns.
"The meeting was satisfactory," the source added, when asked about the outcome of the meeting.