An Optical Transport Network (OTN) mode management system includes a controller communicatively coupled to at least one OTN port. The controller is configured to operate an OTN line Optical channel Data Unit level k (ODUk) mode management system for the at least one OTN port, and the OTN line ODUk mode management system is configured to support different multiplexing scenarios on the OTN port with no loss of control plane packets on aggregated links. A network element includes at least one port with a plurality of lines associated therewith, a controller communicatively coupled to the at least one port, and an OTN line ODUk mode management system executed on the controller for managing the plurality of lines on the at least one port. A method includes configuring and dynamically managing modes of a plurality of OTN lines in a link.