I have prostatitis (bacterial infection). i am on antibiotics, i ejaculate after every three days. does this activity disrupt the treatment ?

No, ...: Masturbation would not affect the effects of antibiotics but may exaggerate the existing voiding symptoms. So, it's logical to give the inflamed area (if any) a rest by refraining from doing it. Note: If you indeed had bacterial prostatitis, taking effective antibiotics should improve Sx in 2-3 days. If not, consider misdiagnosis or ineffective antibiotics. More? Ask Doc timely.