The prosecutor conducting the investigation of corruption in the General Services Administration disagreed today with the sentencing practices of the judge hearing the GSA cases here.

It started when the prosecutor, Asistant U.S. Attorney Daniel M. Clements, recommended a year-and-a-day prison term for former GSA store manager Manuel M. Cumes, 32, of Springfield, Va., who had pleaded guilty to defrauding the federal government. Cumes and his family broke into tears, crying so hard that some of the court clerks started crying too.

U.S. District Judge Frank A. Kaufman then sentenced Cumes to four months in a work-release program.

At a later sentencing session today, Clements told Kaufman several times he had considered all problems of each defendant in working out plea agreements. The recommendations for incarceration are part of the plea agreements.

Kaufman told Clements three times that the judge, rather than the prosecutor, determines the sentence.

The judge then told Johnnie Johnson Sykes, 32, of Oxon Hill that he had to go to jail as a deterrent to others and in fairness to other former GSA employes already sentenced.

He gave Sykes, who also had pleaded guilty to defrauding the government, 3 1/2 months in jail and about eight months on probation.

Clements had recommended a nine-month jail term.