WASHINGTON (Reuters) - Special envoy to Sudan Scott Gration is stepping down after helping to lay the groundwork for the African country's peaceful secession referendum last month, the White House said Thursday.

Gration, a retired Air Force general and Africa specialist who President Barack Obama selected to guide Washington's policy on Sudan, will be nominated to become the new U.S. ambassador to Kenya, a White House statement said.

We would like to stress that his departure in no way indicates that this administration is walking away from the many challenges we still face in Sudan, particularly in Darfur," the statement said.

Gration helped apply U.S. pressure on both Khartoum and the south Sudan government to finish preparations for the January referendum in which south Sudan's voters overwhelmingly chose to split off and form Africa's newest country.

Gration, often believed to be at odds with other Obama administration officials, also promoted incentives for Khartoum, capped by a promise to begin work to remove Sudan from the U.S. state sponsors of terrorism list and eventual full normalization of ties.

Some activists have criticized Gration's policy for going too easy on Khartoum, noting that violence continues in the western region of Darfur where the United Nations believes as many as 300,000 people died after non-Arab rebels rose up against Sudan's government in 2003.

But the Obama administration has in recent months added to its team in Sudan, naming veteran diplomat Princeton Lyman to help the north and the south work out key remaining issues including the division of oil profits and Dane Smith, another longtime U.S. envoy, to work on the Darfur issue.

The United States has pledged to be among the first countries to recognize south Sudan's formal independence in July and will step up aid assistance to help the young nation find its feet.

(Reporting by Andrew Quinn and Caren Bohan, editing by Will Dunham)