Corruption has hindered the effectiveness of customs administrations in many developing countries. In the 21st century, a new problem has arisen which is the rise of international terrorism. Usually, these criminal corruption activities will happen at the border points of a country. This is where the criminal operators offer bribes to the customs officials to allow them to smuggle illegal items into the country. This has posed a huge risk to both the internal and international securities of many countries. This paper seeks to investigate the factors that may influence corruption in organizational procedures that occur in Malaysia. Given the importance of government agency and its accountability, internal control and discretionary power, this paper focuses on these factors in the effort to combat corruption, increase moral awareness and narrow the opportunities for corrupt practices. Specifically, this study found that there are significant relationships between the level of accountability, internal control, discretionary power and the perception on corruption. The result also indicated that corruption flourishes in a situation where the accountability of agents to the principal is weak, when agents have low internal control and when the agents have great discretion.