The Research and Development (R&D) organisations by the nature of business activities will have to deal with higher level of uncertainty than that of a non R&D organisation. This has an effect on the organisational goal setting (Chenhall, 2003), planning system (McCaskey, 1974), and control systems (Hopwood, 1972; Simons, 1987; Williams et al, 1990; Chenhall, 2003, Bisbe and Otley, 2004). Therefore, question had been raised regarding the suitability of existing management control systems for such organisations (Cooper et. al., 1981; Abernethy & Stoelwinder, 1991; Chenhall, 2003). In recent years there has been an increasing interest on investigating the management control systems (MCS) in relation to R&D activities (Rockness & Shields, 1984; Tatikonda and Rosenthal, 2000; Ditillo, 2004). The major objective of this study is to propose a MCS framework for a R&D organisation in the light of four key elements of MCS, namely Desired Ends, Actors, Control Implementation, and Control Tools. The study concludes that the use of those elements may differ between low and high level of uncertainty that an organisation deals with. Two sub elements of Desired Ends (Directional and Yardstick) identified in this study are found to be complementary in a low level of uncertainty while the emphasis need to be placed on Directional under a high uncertainty situation. The consideration regarding Actor, in which the study identified five sub elements; Behavioural, Motivation, Domination, Decision Space, and Power Source are also different along the level of uncertainty of the environment. In addition, the emphasis on the importance of Control Implementation with regard to the timing and the use of formal and informal control type are found to be different along the level of uncertainty as well. Finally, the dimension and the value of control tools are used differently in those two distinctive situations.