Cardinal Roger Mahony of Los Angeles strongly denies the allegations, which were made last month, but relate to an incident more than 30 years ago.
He said he had asked for investigations by both police and the church. The cardinal is believed to be the most senior sitting American church official to be accused of sexual misconduct, in a series of scandals over the past few months.
Priests in several states have been removed since the trial earlier this year of defrocked Boston priest John Geoghan, who was sentenced to prison for child molestation. The Church is facing mounting criticism following allegations that it covered up cases of abuse for decades.
'Hurtful allegations'
The latest accusation of sexual abuse was made by a woman in Fresno who told church officials there last month of the alleged assault.
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She said she had been knocked unconscious in an incident at a Catholic high school in 1970 when Cardinal Mahony was a priest in Fresno.
She alleged that when she came to, Father Mahony was hovering over her.
"I know people are not going to believe it, but it happened to me," she said. In a statement late on Friday, Cardinal Mahoney said his personal integrity demanded that he refute the charges.
"Such allegations are hurtful and troubling to me. Yet I continue to pray fervently for those who make them," he said. The Los Angeles diocese, which numbers five million Catholics, has opened an investigation into the case and interviewed the woman complainant.
A police investigation is also under way, according to the Los Angeles Times.
LA police have said they are investigating reports that the diocese removed six to 12 priests accused of sexual abuse in cases dating back up to 10 years.
Suicide
In another development, a Catholic priest accused of sexually molesting a girl two decades ago has been found dead after apparently committing suicide.
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In Ohio, the body of 48-year-old Father Don Rooney was discovered slumped in his car in a shopping centre car park in Cleveland on Thursday with a gunshot wound to the head, police said.
A suicide note was reported to have been found nearby. The allegations, which came to light after the unnamed woman contacted church leaders, have not been fully investigated or substantiated.
The alarm was raised after Rooney failed to appear at a meeting with local church officials.
See also:
04 Apr 02 | Americas NY church reveals 'sex abuse' list 24 Mar 02 | Americas Paedophile priests in US face crackdown 04 Apr 02 | Americas Vatican sued in sex abuse cases 21 Mar 02 | Europe Pope denounces 'evil' sex priests 12 Mar 02 | Americas Church agrees sex abuse payout 02 Apr 02 | Americas Paedophile priests 'damage church' 08 Jan 02 | Europe Vatican acts on paedophile priests 11 Jul 98 | Americas Church pays $31m to sex abuse victims |
Source: BBC Who is terrified of reporting about the bad rabbis