Fifteen senior immigration officers were sacked on Friday as new measures were announced to authenticate all security documents.
An audit of all national IDs and passports issued within the last two years will be carried out.
All national IDs not collected within three months will be destroyed to prevent them from falling into the hands of terrorists and illegal immigrants.
About 350,000 have not been collected.
Mr Lenku said those sacked because of irregularities in issuing of passports and IDs will be prosecuted.
The sackings follow the findings of a security audit ordered by Mr Lenku after the Westgate terrorist attack on September 21.
“We have fired 15 senior and middle level officers who were implicated in issuing Kenyan identity documents to illegal immigrants” said Mr Lenku.
He revealed that the purge would be extended to other departments in the ministry, the police and prisons.
Mr Lenku said the audit revealed loopholes that terrorists exploited to plan and execute the attack.
The audit also showed that “waiting cards,” issued to applicants before an ID card is processed were being abused by foreigners and would be invalidated after three months. (READ: More civilians to carry guns)
At the same time, Mr Lenku announced six officials who would revive community policing, a crime fighting strategy established in 2005 but that has since become moribund.
The six are former administrator Joseph Kaguthi (chairman), Kenya Airways boss Titus Naikuni, security expert Simiyu Werunga, Ms Nurie Abdillai, Mr Salim Ndemo and former Director of Criminal Investigations Francis Sang.
“Community policing is anchored in the constitution which requires the police to promote relationship with the broader society,” said Mr Lenku.
The government has also said it will introduce the Nyumba Kumi concept he said and added: “It does not necessarily mean 10 households. It means a cluster of households, like residents’ associations and gated communities,” he said Mr Lenku.
He also said plans to send Somali refugees home were in progress. “Some of them have abused our hospitality and launched terror attacks from the camps,” he said.
“The government is working closely with Somalia government and the UN refugees’ agency to ensure the repatriation is as smooth and humane as possible,” he said.
It has come to light that the Westgate attack, which killed at least 67 people and injured 240 was planned at the Daadab refugee camp.
Kenya hosts more than 600,000 refugees, the biggest number in the world. Most of them are from neighbouring Somalia. The government wants them moved to either parts of Southern Somalia. (READ: Nyumba Kumi plan to curb abductions in Murang'a)