Some 100 soldiers arrived from Juba in an Ocean Airlines airliner and 100 more were expected to jet in.
The government withdrew the troops following the sacking of a Kenyan general in-charge of the United Nations Mission in South Sudan last week.
UN Secretary General Ban Ki-moon fired Lt Gen Johnson Ondieki over "serious shortcomings in the leadership" of UNMISS, leading to a chaotic and ineffective response to the violence.
UNMISS is a peace keeping contingent comprising of troops from various countries.
Kenya withdrew her troops in protest over the sacking of Ondieki.
Major Gen Benjamin Biwott in-charge of Eastern Command said the withdrawal will continue until all soldiers are back.
"The exercise will continue depending on how the UN will provide logistics," Biwott said.
He said Kenyan troops have been involved in more than 40 peace missions and are willing to help South Sudan to regain stability.
"But decisions and agreements are made at another level. The President has directed that we withdraw and we have to comply with the directive," Biwott said.
The soldiers went into the war-torn country in May and were spread in three regions, including the capital Juba.
Kenya had deployed various professionals including doctors, engineers and counsellors among others to the country to offer humanitarian support.
A UN internal report revealed that UNMISS failed to protect civilians last July.
Humanitarian workers were subjected to violence, including rapes and killings.
The government said sacking Ondieki would not address the root causes of the "unfortunate incidences" in South Sudan.