Spotlight: A Woman Alone With The IRA investigated the republican movement's handling of sexual abuse allegations against a suspected IRA member.
Maíria Cahill waived her right to anonymity to tell how the republican movement responded to her allegations.
The programme won news and current affairs programme of the year and scoop of the year.
Spotlight reporter Jennifer O'Leary also won the award for broadcast journalist of the year.
In the programme shown last October, Ms Cahill claimed she was raped by a suspected IRA man when she was a teenager, and that the IRA later helped to cover up the alleged abuse.
BBC Radio Ulster's Stephen Nolan was named news and current affairs presenter of the year.
The Arts Show on BBC Radio Ulster won entertainment programme of the year.
BBC Radio Foyle's Mark Patterson won the award for speech radio broadcaster of the year.
BBC Northern Ireland director Peter Johnston said: "We are extremely proud of the awards received at this year's CIPR ceremony and I would like to congratulate all the teams and individuals who won and were nominated.
"2014 was a very eventful year for us across TV and radio, and receiving acknowledgement for this content is testament to the dedication of our teams who continually strive to provide audiences with high quality programmes."
BBC Northern Ireland current affairs programme Spotlight has won three CIPR NI Media awards.