A top federal career bureaucrat resigned his $47,500-a-year post yesterday and attributed the move partly to the frustrations of the federal personel system and other elements of the "bureaucratic swamp."

Dr. Harry Cain, director of a key health planning program in the Department of Health Education and Welfare, called a press conference to announce the decision. At the same time he put in a plug for President Cater's efforts to streamline the personnel system and give managers such as Cain more flexibility in their use of the workforce.

Cain's boss, Dr. Henry A. Foley, and others in the program indicated they shared Cain's views on the need for restructuring the personnel system. They also emphasized that they felt Cain had done a good job as director and that his decision to resign was entirely his own.

While Cain singled out the federal personnel system, he also included as problem areas in the "swamp" such items as procurement, reports clearance and regulation development.

He did not go into detail yesterday about the problems, but statements previously attributed to him had criticized managers' inability to move employes around to positions where they were most effective.

After 16 years in government, and two years with this program, Cain indicated, he now is looking forward to the chance to "explore other options."

As director of the Bureau of Health Planning and Resources Development, Cain had almost 300 employes and a budget of about $150 million for projects plus a $3 billion loan account. The program is part of a process that controls the expansion of hospitals, special equipment and services.