A procedure is developed to probe the changes in the functional interactions among neurons in primary motor cortex of the monkey brain during adaptation. A monkey is trained to learn a new skill, moving its arm to reach a target under the influence of external perturbations. The spike trains of multiple neurons in the primary motor cortex are recorded simultaneously. We utilize the methodology of directed transfer function, derived from a class of linear stochastic models, to quantify the causal interactions between the neurons. We find that the coupling between the motor neurons tends to increase during the adaptation but return to the original level after the adaptation. Furthermore, there is evidence that adaptation tends to affect the topology of the neural network, despite the approximate conservation of the average coupling strength in the network before and after the adaptation.