Williams, head of the worldwide Anglican Communion, made the statement during a visit to Egypt, the Times of London reported.
Starting next month, gay couples in Britain can register as civil partners, giving them some of the rights of married couples. About 400 Church of England priests are believed to be living in homosexual relationships and planning to seek legal status.
The Church of England does not bar homosexuals from the clergy but requires them to be celibate.
"If it can be established that a priest seeking to register a civil partnership is in fact active in a sexual union, then that priest is liable to the discipline of the Church," Rowan said.
The Rev. Richard Kirker of the Gay and Lesbian Christian Movement, told the Times he believes that gay clergy will register their unions secretly to avoid "an inquisition."