Struggle against Communisn
Wielgus was named by Pope Benedict to succeed the retiring Cardinal Jozef Glemp, a figurehead of the long struggle against communism, in one of the most influential positions in overwhelmingly Catholic Poland's church hierarchy.
Soon after his appointment, Polish media reported that Wielgus had informed on fellow clerics for around 20 years from the late 1960s.
Wielgus formally took up his job on Friday and is due to be ceremonially invested at a mass on Sunday attended by the president and other government officials.
He started by denying the allegations. But a special Church commission said in a statement there was sufficient evidence to confirm he was a willing informer.
"There are plenty of important documents which confirm Wielgus' willingness to ... cooperate," the commission said.
Wielgus, however, gave no indication that he would resign, a step widely expected by Church commentators and some Church officials.
The Polish Catholic Church said it had been the Pope's decision to appoint Wielgus, and that it could not make any comment about his resignation.
The Vatican says it examined the archbishop's past before the nomination and has so far refused to make any further comment.
But an opinion poll released on Friday said a majority of Poles believed he should not take up his post.
In the 1980s, the church supported the pro-democracy Solidarity movement and, along with Polish-born Pope John Paul II, played a crucial role in bringing down communism in 1989.
Church historians however say that up to 10 per cent of the clergy may have cooperated knowingly or unknowingly with the Soviet-controlled communist authorities. The church has so far refused to make their names public.
Commentators say the scandal is the biggest crisis for the Polish church in the last 17 years.
"The whole issue is a terrible embarrassment," Tomasz Wiscicki, a religious affairs analyst, said. "Poles are now testing their relations with the Vatican without John Paul."
An editorial in the daily Dziennik said it would be a "moral scandal" if the archbishop did not resign.