Backgrounds: Since decentralization year 2001, various innovations have been made by the districts or municipalities, especially on delegating broader decision space for management of community health centers to meet demands for qualified medical care. Objective: This study aimed to determine the relationship on autonomy level at health centers (decision space) of employee motivation. The motivation of employees was related to the concept of Motivating Potential Score, that composed of Skill Variety, Task Identity, Task Significance, Autonomy, and Job Feedback. Methods: tt was an observational study with a cross sectional design, carried out at Puskesmas Depok /I (150 type), Sleman District, Yogyakarta Province and at Puskesmas Bangil (self-management type), Pasuruan District, and Puskesmas Karangsari (free type), Blitar Municipality both in East Java Province. The study was done from May to December 2009. Respondents were employees at public health centers taken by random sampling to proportional size. Analysis were to assess the status of autonomy relationship with employee motivation at public health centers, tested by anova and combined with qualitative analysis from in-depth interviews to heads of the centers. Results: Results showed that most employeer motivation at each type of health centers was cathegorized as fairly autonomy status for public health center with 150 (62.5%), self-management (72%) and free type (75.7%). The Anova test were F = 1.450 at p-value = 0.240 (p > 0.05). Hence, it could be said there was no difference on employee motivation at health center type, 150, self-managed and free type. Recommendations:This study recommends that heads of community health centers should be able to encourage development of intrinsic motivation to create leadership to give inspiration for employees and supportive work environment, empowering employees, delegating meaningful work and enhancing employee competency.