Although over 4,000 people were arrested in raids in the past week, police said only 447 are currently being held.
The Somalian ambassador to Kenya, Mohamed Shake Ali, confirmed 82 people were deported.
The security operation has largely focused on a Somali enclave in Eastleigh, a suburb of the Kenyan capital Nairobi. Six people were killed in Eastleigh in 2011 when a grenade exploded. The Kenyan government suspects the Somalian militant Islamist group al-Shabab has the support of some Somalians in the suburb.
Al-Shabab militants took control of a Nairobi shopping mall in 2013 in a four-day incident in which 67 people died.
The arrests, which involved taking suspects to police stations and stadiums for interrogation, was condemned by some leading clerics and Kenyan parliament members, who claim the police unfairly targeted Somalis. The United Nations High Command for Refugees said Monday it was denied access to arrested asylum-seekers.