The Inspector-General of Intelligence has accused State Security Agency director-general Arthur Fraser of threatening him and trying to block an investigation into "serious" allegations against the spy boss.

Dr Setlhomamaru Dintwe said on Wednesday that Fraser had allegedly launched unlawful attempts to block his investigation‚ forcing him to go to court to seek urgent legal protection.

"The Director-General has threatened and intimidated me on more than one occasion‚" he said in a statement.

Fraser was implicated in the alleged mismanagement of state security funds in a book by author Jacques Pauw‚ who in The President's Keepers claimed that a huge sum of taxpayers' money was wasted on a project headed by Fraser. Fraser dismissed the allegations.