The government's new program of paying cash bonuses to selected federal employes, which has been under fire for months in Congress, has taken additional flak from a new source: the federal workers eligible for the bonuses.

In a survey of about 1,000 members of the government's Senior Executive Service, half of the respondents said they think a disproportionate share of the bonuses goes to top agency executives at the expense of deserving workers in mid-level ranks.

Further, 45 percent said they knew of instances where bonuses were given to "management favorites" instead of more deserving people not in favor at the top. A third said the bonuses are not generally paid to the best workers.

The result, according to the survey taken by the Merit System Protection Board, an independent agency that is supposed to guard against political abuse of the federal workforce, is that "the majority of [top federal] executives does not believe a real opportunity for monetary reward exists."

The survey showed that while 70 percent of the executives polled had received high performance ratings from their superiors, less than 30 percent think they are likely to receive a bonus in the next year.

The bonus system, under which federal employes can receive up to $20,000 in recognition of superior performance, was one of the chief sweeteners Congress included in the 1978 Civil Service Reform Act, which established the Senior Executive Service to take the place of the old Civil Service "supergrades" (GS16 to 18).

Federal employes who join the Senior Executive Service -- chosen through an annual competition -- give up some of the job protections of the traditional Civil Service. This change was designed to give agency heads more flexibility in transferring veteran executives and putting their own team in significant agency jobs. To convince federal employes to accept the change, Congress offered SES members new job opportunities and the chance for bonuses.

But when the first bonuses were paid last year, reports to surface about apparent favoritism. At the Small Business Administration, for example, the board chosen to divvy up bonuses saw to it that all eligible board members received them. These reports led to efforts in Congress to cut or end the bonus program.

The protection board's survey involved questionnaires sent 1,500 of the 8,500 SES personnel in the executive branch. About 1,000 executives responded.

The survey also found that about 25 percent of respondents said they will leave government service in the next two years "if they have their own way." Twenty percent said there is a 50-50 chance they will quit the government before 1983.

The chief reason seems to be money; government employes are unhappy with the $50,112.50 lid on career personnel salaries, and do not expect to gain much through the bonus system.

Still, 91 percent of those surveyed said they are satisfied with the nature of their jobs and the work they do. And more than half said they think their work is appreciated by management.