A number of allegations of sexual abuse have been made against the Pacific islands archbishop, Anthony Apuron, which he denies.
The 70-year-old will retain his title as Archbishop of Agaña, according to USA Today.
He has not been charged with any crime and there has been no civil lawsuit filed against him.
Hong Kong-born Archbishop Savio Tai Fai Hon, now second in command of the Vatican's Congregation for the Evangelization of Peoples, has been given temporary authority to govern the Guam archdiocese.
Archbishop Apuron has been in charge since 1986.
There has not been another appointment like this made in a US territory.
Almost six-out-of-seven residents of the Archdiocese of Agaña are Catholic, which equates to around 157,000 parishioners.
Over the weekend, Pope Francis announced that he had signed new rules for the removal of any bishop who failed to respond to allegations of any form of abuse.
Under these new guidelines, the Vatican has the power to investigate a bishop thought to be negligent.
The bishop would have a right to respond.
Five years ago, Guam removed its statute of limitations on prosecuting sex crimes against children.
Deacon Steve Martinez, former coordinator of a Guam church group charged with reviewing sexual-abuse allegations involving clergy, has spoken out.
He has been reported saying that Archbishop Apuron purposely kept the Guam archdiocese's sexual-abuse policy less stringent that it could have been.
Following his comments, the archdiocese said it would take action against Mr Martinez and would appoint an independent investigator to look into the accusations.
