In a telephone conversation, Ban urged Kenyatta to continue to abide by a November 2013 agreement with the Somali government and the UN High Commissioner on Refugees "as a basis for the voluntary return of Somali refugees in safety and dignity."
Kenya hosts around 600,000 refugees, some of whom have lived in the country for a quarter century.
It says it wants to close the Dadaab and Kakuma camps because they have become breeding grounds for the Al-Qaeda-linked Al-Shebab militant group and centers of crime and contraband.
Ban also said he supported a proposal by the UNHCR for a "high-level bilateral review on the refugee situation," adding that High Commissioner on Refugees Filippo Grandi would travel to Nairobi at the end of May with deputy UN Secretary General Jan Eliasson.
"They look forward to discussing this issue forward with the government of Kenya, and will underline the readiness of the United Nations to garner the support of the international community in addressing Kenya's refugee challenges, with consideration for the host communities in Kenya as well as the sub-regional security concerns," Ban said, according to a UN statement.