Purpose: This paper intends to explore the measure for aligning the goals of researchers toward achieving organizational R&D targets. The paper also explores the significance and ordering of R&D outputs and the factors that influence generation of R&D outputs, from the perspective of researchers working in the Indian public sector organizations. Design/methodology/approach: Data were collected in five Indian R&D laboratories, and weighted average method Spearman correlation coefficient and rank regression were utilized for the analysis. Findings: The findings indicated that various groups of researchers prefer to target different R&D outputs and not all the factors are considered as equally significant in influencing the generation of R&D outputs. Further, the R&D organization should include preferred real factors while policy making for achieving collaborative efforts toward fulfilling organizational objectives. The set of selected R&D outputs and influencing factors were also ordered according to the average rankings given by the researchers. Practical implications: The findings can help R&D managers to identify the expectations of the researchers and include their preferences in R&D Planning. The study could be extended to a larger dataset of researchers working in other government as well as private R&D organizations. Originality/value: Hardly any studies were found that explored the preferences of researchers with respect to R&D outputs and influencing factors with respect to the Indian public sector R&D laboratories. © 2022, Emerald Publishing Limited.