As well as searching a couple of main Church offices and a cardinal's home, police had drilled holes in two archbishops' tombs, said the Church.
Prosecutors said the raids were over alleged "abuse of minors committed by a certain number of Church figures".
Belgium is one of many countries where the Church has been hit by sex scandal.
In April, the Bishop of Bruges, Roger Vangheluwe, resigned after admitting he had sexually abused a boy more than 20 years ago.
'Da Vinci Code'The Vatican has summoned the Belgian ambassador to the Holy See to voice anger over Thursday's raids.
Police in Leuven seized nearly 500 files and a computer from the offices of a Church commission investigating allegations of sex abuse.
They also searched the Church's headquarters, the Brussels archdiocese in Mechelen, north of the Belgian capital.
Bishops holding a meeting there were barred from leaving the premises for several hours and had their mobile phones confiscated, said Church officials.
Investigators made holes in the tombs of two former Belgian primates at Mechelen cathedral, and sent down cameras in search of hidden documents, without success, said a Church spokesman.
In a statement, the Vatican expressed "shock over how the searches were carried out by Belgian judicial authorities and indignation over the violation of the graves of the Cardinals Jozef-Ernest Van Roey and Leon-Joseph Suenens," reports AFP news agency.
The raids had been the stuff of "crime novels and The Da Vinci Code", said the Church's leader in Belgium, Archbishop Andre-Joseph Leonard.
"We are surprised it went as far as drilling into tombs in the cathedral," he told a news conference in Brussels on Friday.
A spokesman for the Belgian prosecutor in the Belgian capital told news agency Reuters that investigators partially opened one tomb in the cathedral after someone mentioned work had recently been carried out on the grave.
Officers also raided the nearby home of the recently retired Archbishop of Belgium, Cardinal Godfried Danneels.
He was not interrogated but a personal computer and some paperwork was confiscated.
The Vatican said the raids had led to the "violation of confidentiality of precisely those victims for whom the raids were carried out".
The Catholic Church in Belgium has apologised for its silence on abuse cases in the past and Archbishop Leonard has promised a policy of zero tolerance.
SIC: BBC