Iran's budgeting reform has followed a defined plan of budgeting implementation from its inception in the year 2002. Growing from a desire to improve services and the efficient utilization of resources has begun to penetrate all levels of the government. The purpose of this paper is to evaluate the challenges and limitations of budgeting and its accounting method in governmental organizations. The research method in this paper is a field study. Information were collected by referring to governmental organizations and using their documents, and interviewing the top managers and also the vice-presidents of the organizations as well as the staff in the financial departments of these organizations. The results of this research show that there are some problems due to the private deposits and incomes, and some solutions were suggested to remove the mentioned problems. Doing studies in this field can help us to reform the budgeting system and to reduce the obstacles and solve the problems.