The Executive Order is properly and lawfully issued by President Uhuru Kenyatta, Attorney General Kihara Kariuki has said.
Kariuki was responding to Chief Justice David Maraga, who claimed that the President made and error by interfering with the independence of the Judiciary when he signed the order.
Maraga faulted Uhuru's Executive Order, in particular, placing the Judicial Service Commission under a state department.
The CJ said the JSC is part of the Judiciary, a government branch that can't be assigned functions by the Executive.
But in a statement on Thursday, Kariuki said the statement by Maraga is premised on a misunderstanding of the order.
"Nothing in the Executive Order is intended to undermine any independent arms of government or institutions or to cause any confusion to the public," he said.
"The Executive Order seeks to provide clarity to ministries and government departments on their responsibilities with respect to the necessary and inevitable inter-agency linkages and liaisons."
Kariuki said it is the duty of the President to define for ministries and government departments such responsibilities and mechanisms for fostering policy coordination and the building of synergies between all arms of government.
"This is no way infringes on the autonomy of independent offices and constitutional commissions, nor does it violate the doctrine of separation of powers and roles that is a key pillar of the Constitution," he said.
"There is no provision in the Executive Order with the express implicit purport of restructuring the Judiciary or assigning functions."
In the order signed on May 11, the President assigned functions and institutions among ministries and state departments, superseding the Executive Order No. 1 of 2018 (Revised) issued in July 2018.
It contained portfolio responsibilities and changes made in the structure of government.
Uhuru specified functions of the constitutional commissions, independent offices, the Judiciary and Parliament.
But Maraga said the order cannot restructure or assign functions to the other co- equal and co-substantial arms of government and independent commissions.
