Official sources said the inquiry will cover the whole process of preparing the list of 50 most wanted fugitives at different stages and pin-point the officials responsible in including the name of Wazhul Kamar Khan, who was arrested last year for his alleged role in the 2003 Mulund train blasts.
"It could have been a cut and paste job at some stage. We will find out who is responsible for it," a source said. "Wazhul Kamar Khan" a name is at number 41 in the list of 50 fugitives.
The list of most wanted fugitives, which was given to Pakistan at the Home Secretary level talks in March, has names of Lashkar-e-Taiba founder Hafiz Saeed and dreaded terrorist Zaki-ur-Rehman Lakhvi besides others.
The Home Ministry is also seeking a report from the Maharashtra Police about the status of Khan's case and his current location.
The list was prepared in consultation with Maharashtra Police, National Investigation Agency and Central Bureau of Investigation.
Khan has been living in Mumbai suburb Thane's Waghle Estate with his mother, wife and children, after he was let off on bail, police sources said.
He was also involved in the 2003 Vile-Parle and Ghatkopar blasts besides the 2002 Mumbai Central station blasts.
The Vile Parle, Mulund and Ghatpokar cases have been clubbed together and the trial is yet to begin, the sources said.