Manalo took over Iglesia ni Cristo, or Church of Christ, after the death of his father and the church's founder, Felix Manalo, in 1963. The church is believed to have millions of members but does not disclose the figure.
Manalo died of a heart attack in his Manila home on Monday, the church's spokesman Bienvenido Santiago said.
The church was founded in 1914 when Felix Manalo resigned as minister of the Seventh-Day Adventist Church after questioning the observance of Sabbath on Saturdays. He experienced what he claimed to be a call similar to those of ancient prophets.
Iglesia ni Cristo rejects the Christian doctrine of trinity and believes Christ is one of several prophets.
It is considered the largest indigenous church that originated from the Philippines and the largest independent church in Asia.
To the family of late Ka Erdy Manalo our condolences and also to the Iglesia Ni Cristo family our condolences. May he rest in peace.