He had been named to succeed the retiring Cardinal Jozef Glemp, a figurehead of the long struggle against communism, in one of the most influential positions in Poland's church hierarchy. Dr Glemp will now retain the archbishopric pending a new appointment.
In a statement issued on Friday, Dr Wielgus appeared to back down from his earlier denials and to open the door for the Pope to remove him from office.
Soon after his appointment, Polish media reported that Dr Wielgus had informed on fellow clerics for around 20 years from the late 1960s.
A special church commission said in a statement there was sufficient evidence to confirm he was a willing informer. Dr Wielgus formally took up his job on Friday and was due to be ceremonially invested at a mass today attended by the president and other government officials.