Covert timing channels are used to transmit information through computer networks in a seamless or secret way. Inter-packet gap and packet reordering are among techniques of encoding information in covert channels. Several works on evaluating capacity and robustness of covert channels are published in which the channel is evaluated using real environment field tests or by means of computational methods. Real environment field test lacks the repeatability property of the test and computational method is normally too simple to enable one to evaluate the channel under desired circumstances. In this paper, a new model for an end to end communication channel in the Internet is proposed using Petri-Net modeling. The model is able to inject different types of noises such as packet loss, packet reordering, and jitter to a given traffic. The model was used to implement a controlled hybrid covert timing channel under desired noise levels. Then, the capacity and robustness of the covert channel was measured using different noise scenarios. The model proves itself effective for further covert channel evaluation in given circumstances.