Fault tolerance has become more and more important in the development of autonomous systems with the aim to help the system to recover its normal activities even when some failures happen. Yet, one of the concerns is how to analyze the reliability of a fault tolerance mechanism with regards to the collaboration of multiple agents to complete a complicated task. To do so, an approach of fault tolerance analysis with the colored time Petri net framework is proposed in this work, where a task can be represented by a tree of different concurrent and dependent subtasks to assign to agents. Different subtasks and agents are modeled by color tokens in Petri network. The time values are added to evaluate the processing performance of the whole system with respect to its ability to solve a task with fault tolerance ability. The colored time Petri nets are then tested with simulation of centralized and distributed systems. Finally the experiments are performed to show the feasibility of the proposed approach. From the basics of this study, a generalized framework in the future can be developed to address the fault tolerance analysis for a set of agents working with a sophisticated plan to achieve a common target.