All refugees in the Dadaab camp will be repatriated to Somalia by May next year, the government has said, despite calls against the move.
Interior PS Karanja Kibicho said the first batch of the refugees will have been moved by November.
The government announced on Friday it had disbanded the department of refugee affairs, the first step in closing Dadaab and Kakuma camps in Garissa and Turkana counties respectively.
Kibicho cited a heavy economic, security and environmental burden and Kenya's national security interest.
But he told editors at a Nairobi hotel on Wednesday Kakuma camp will not be affected, as it "does not pose any threat".
He said it is only Dadaab camp that has remained a "source of headache" for Kenya; the camp has a terror cell and "thriving illicit trade".
"We are assuring the world that there will be no Dadaab refugees by May. This is an undertaking we are making as a government," he said.
He said the government has put in place plans to make sure those targeted do not "escape" from the camps to neighbouring counties.
Global humanitarian and human rights agencies lashed out at Kenya for going against its international obligations in protecting the rights of refugees and displaced persons.
They include Amnesty International, Human Rights Watch, the Kenya National Human Rights Commission, Save the Children, World Vision, Oxfam, International Rescue Committee, Danish Refugee Council and the Lutheran World Federation.
The agencies said the announcement will have far-reaching implications on thousands of refugees and asylum seekers who have called Kenya a place of refuge.
But Kibicho maintained that Kenya will not turn back on the move as $10 million (Sh1 billion) has been set aside for the exercise.
The Principal Secretary said the international community has "abdicated" its responsibility in providing funds for the refugees.
"At least $100 million (Sh10 Billion) was pledged for refugees in the last few years. Kenya has only gotten Sh1 billion of this," he said.
But he noted that the government is not taking the move to solicit funds from the international community.
"Not at all. Even if they gave us one billion dollars per refugee... We do not want it," he said. "We want these people to go back. Our national interest is superior to our international obligations."
Kibicho accused NGOs of being behind the slow pace of refugee returns to Somalia; he said they have hampered efforts to effect the Tripartite Agreement signed in November 2013.
The agreement by the UN refugee agency, Kenya and Somalia provides a road-map in which the refugees can go home in a humane, safe and voluntary process. At least 14,000 refugees have since returned.
Dadaab and Kakuma camps house about 400,000 people; Daadab alone had about 340,000 refugees while Kakuma had more than 55,000 in UNHCR data released in September 2015.