An increasing bandwidth demand has mandated a shift to the time and wavelength division multiplexing (TWDM) techniques in optical access networks (OAN). Typical TWDM scheduling schemes consider scheduling of the optical line terminal receiver only. In this paper we have identified an additional collision domain that is present in TWDM schemes that offer security, in addition to bandwidth flexibility. Scheduling of the identified collision domain is termed as group scheduling. We illustrate that consideration of receiver scheduling only (as done in typical TWDM schemes) severely affects their throughput when implemented on flexible and secure TWDM architectures. A novel media access control protocol has been proposed in this paper that considers the multiple collision domains. Through simulations, we are able to illustrate that the proposed scheme achieves a high throughput. A theoretical upper bound of throughput has also been derived to explain the simulation results. Complexity reduction of the proposed scheme has been illustrated, thereby making it an attractive proposal.