Mrs Brooks and her racehorse trainer husband Charlie revealed the charges in a statement in which they criticised the decision by the Crown Prosecution Service.
They said: "We have this morning been informed by the Office of the Department of Public Prosecutions that we are to be charged with perverting the course of justice.
"We deplore this weak and unjust decision.
"After the further unprecedented posturing of the CPS we will respond later today after our return from the police station."
Four other people are also to be charged with conspiracy to pervert the course of justice in connection with the inquiry, including Mrs Brooks's personal assistant Cheryl Carter and Mark Hanna, head of security at News International.
The charges include conspiring to conceal material from Scotland Yard detectives, conspiring to remove boxes of material from the archive of News International and conspiring to conceal documents, computers and other electronic equipment from detectives.
Mrs Brooks faces three conspiracy charges. The others all face one charge each.
The charges are the first to be brought following Scotland Yard's multi-million pound investigations into phone-hacking, computer hacking and corruption, which have led to 50 arrests.
Today's decision to bring charges comes just days after Mrs Brooks lifted the lid on her close relationship with the Prime Minister at the Leveson Inquiry into press standards.
Mrs Brooks, a high-flyer in Rupert Murdoch's News Corp media empire, is one of the highest profile figures in the newspaper industry.
She became News of the World editor in 2000 aged 31, landed the top job at The Sun in 2003 and was appointed chief executive of News International in 2009 before quitting in July 2011.
Days later she was arrested over alleged phone-hacking and corruption, offences for which she remains on bail without charge.
She was arrested again in March in connection with the separate perverting the course of justice allegation, with her husband and four others.
Mr Brooks is a former Eton school friend of Prime Minister David Cameron.