This work presents a method and an algorithm for implementing the control of two micro-pumps with tolerance to sensors faults. These micro-pumps are used in a micro-volume deposit system, which is intended to help with biomedical and laboratory tests that involve the use of medical samples. This deposit system performs the suction or deposit of the required volumes of fluid. A requirement for this system is to protect the samples and reagents used in the process for the cost associated with gathering the samples. In this way, the idea is to have a fault tolerant system, which can ensure the integrity of the samples. The method and algorithm are implemented using a technique called analytic redundancy Muenchhof et al. (Eur J Control 15, 2009), which allows reducing the number of physical redundant sensors in a system. For this implementation, we propose the use of a physical sensor and an analytic sensor, using the model of suction-expulsion of the micro-pump from a previous work.