The Higher Education Commission (HEC), Pakistan is one of the prestigious institutions of Government of Pakistan. It sets educational policies for all public sector universities of Pakistan. The aim of this research study is to find institutional bottlenecks and issues of a project. For this purpose, Projects data were collected from Project Directors, HEC personnel's and consultants. Data were collected from 128 universities and institutions of higher learning institution in Pakistan using questionnaires which were designed for this study. To provide the data, respondents were given the choice of being interviewed or self-administer the questionnaires, and send them back to the researcher. After studying and analyzing the data, seven (7) bottlenecks were identified. These include: centralization of the system, delay in approval of projects, procedural delay in funds, accumulation of project, poor coordination and capacities, procedural formalities and poor implementation of policies. © 2011 IEEE.