The CBI registered a case on 27 September 2006 on allegations that Vijayan acquired property in his own name and that of his family members while working as deputy commissioner at the Air Cargo Complex and holding the additional charge of Air Customs at the Calicut airport. which was more than his known sources of income.
He acquired assets worth Rs 79,93,859 between July 2003 and July 2005. The CBI after investigation filed a charge sheet in the case on 30 June 2008 against the accused. The Trial Court found the accused guilty and convicted them. Two accused were acquitted by the court.