Ole Nkaissery said the refugees would be repatriated to their countries of origin or to third party countries for resettlement.
MSF, however lashed out at the decision, urging Kenya to continue its tradition of providing refuge, and move against the inhumane policies of Western nations.
"Rather than endorsing the broken and inhumane policies of Europe and others, now, more than ever, is the time for Kenya and South Africa to embrace and continue traditions of providing safe refuge," said the President of MSF Southern Africa, Dr Mohammed Dalwai, in a statement.
The organisation also urged Kenya to set an example for other countries through its compassionate treatment of those fleeing war and conflict in their home countries.
"If potential solutions are not pursued in Kenya – with the support of the international community - refugees from Dadaab will be forced to return to Somalia where the conditions for their safe and dignified return simply do not exist after 25 years of war. They face terrible options, among which is a perilous journey north to cross the sea to Europe."
"Kenya, South Africa and Africa as whole, can take the lead and set an example to others, including Europe, on how to humanely treat people fleeing war and conflict. Today, it is in the hands of Africans to help the world reclaim humanity," stated Mohammed.
In addition, the United Nations High Commissioner for Refugees has pushed against the move by Kenya, calling on officials to reconsider their decision and avoid taking any actions in contravention of international agreements.
"UNHCR is calling on the Government of Kenya to reconsider its decision and to avoid taking any action that might be at odds with its international obligations towards people needing sanctuary from danger and persecution," the agency was reported as saying in The Star.