NEW YORK — Retired Bishop Thomas Daily, who led the diocese of Brooklyn and Queens for over 13 years, has died. He was 89.

The Brooklyn Diocese said Daily died early Monday at his residence in Douglaston, Queens.

Daily’s successor, Bishop Nicholas DiMarzio, called him a missionary who “never acted out of malice or to further his own self-interest.”

Daily served as Bishop of Brooklyn from 1990 until his retirement in 2003. During that time he weathered racial tensions and financial hardships. As a young priest he ministered to the indigenous people of Lima, Peru.

In his later years, Daily became embroiled in the priest sex scandals. In Boston, where he served in the archdiocese in the 1970s and 1980s, Daily was criticized for failing to thoroughly investigate allegations of priest abuse.