Churches often assume their employees are committed church members and very trustworthy. Accordingly, Churches historically have ineffective or nonexistent internal control systems. Unfortunately, the high level of trust in Churches combined with weaker internal controls, results in increased risks of theft and misappropriation of funds. 

The key elements of an internal control system for a Church should include:

1.) Clear organizational structure with documented policies and procedures. There should be clear and specific positions and responsibilities, including timeliness of duties to be performed. 

2.) Segregation of duties. There are three basic types of financial activities that are performed in a church or nonprofit. These are (1) authorization of transactions, (2) recording of transactions, and (3) custody of assets. A lot of small churches only have one person handling all of their financial affairs. However, you should try if at all possible, to use enough individuals to achieve proper segregation of these activities...for that person's sake as well as the organization. 

The North Carolina Conference of The United Methodist Church maintains an extensive resource of financial policies and internal control training materials on their website.

http://nccumc.org/treasurer/training-materials/

I would recommend these resources for any Church, regardless of denomination.