KeNHA will wait for MPs to pass laws that will allow the erection of toll stations.
The High Court has stopped the State from acquiring land from the Nairobi National Park.
The project will be tackled by Kenya, Uganda and Rwanda as a block.
The project began in 2009 following the award of the tender to China Road and Bridge.
The agency will manage the implementation of the project on behalf of the State.
The first three berths in the port of Lamu will be completed in three years.
The tender will most likely be awarded late next year.
This marks the start of the process of construction of the much awaited bypass.
The security system is jointly funded by the World Bank and the Kenyan government.
The facility is the first to be built in Kenya in the last 80 years.