Higher Education Institutions (HEIs) in Indonesia feel the pressure to provide up to date IT facilities for students, who have been using IT devices and the Internet as part of their life style. One of the facilities needed most is an Academic Information System (AIS) that provides 24/7 access to up to date information and academic transactions. Under the circumstances in 2007, at the HEI of the case study, the AIS must be built in-house regardless of the HEI's being unprepared to develop large scale information systems (IS). IS project development is known to have high risks, even in developed countries. This makes it even riskier in Indonesia, where organizations are less established than in developed countries. This paper presents the risks faced at the project initiation stage of AIS development project and the methods of managing these risks. The methods proposed have been implemented successfully in the HEI of the case study.