In an address to members of the World Council of Churches in Geneva, Dr Williams said that laws specifically targeting gays and lesbians were equivalent to racial discrimination.
"Many societies would now recognise that legal interference with some sorts of consensual sexual conduct can be both unworkable and open to appalling abuse (intimidation and blackmail)," Dr Williams said.
"The existence of laws discriminating against sexual minorities as such can have no justification in societies that are serious about law itself.
"Such laws reflect a refusal to recognise that minorities belong, and they are indeed comparable to racial discrimination."
Dr Williams emphasised that concern for protection of gays and lesbians from violence and intimidation did not imply approval of homosexual behaviour on moral grounds.
"This concern for protection from violence and intimidation can be held without prejudging any moral question; religion and culture have their own arguments on these matters.
"But a culture that argues about such things is a culture that is able to find a language in common.
"Criminalise a minority and there is no chance of such a language in common or of any properly civil or civic discussion."
Reports coming from multiple countries in the Middle East and Africa describe egregious violations of human rights of people accused of being homosexual. In most Muslim countries the existence of homosexuality is not openly acknowledged and gay individuals can be sentenced to prison or corporal punishment, and even capital punishment in some cases.
The same is the case in African countries that are not mostly Muslim, like Cameroon, which is 40 per cent Christian. Uganda, which is 85 per cent Christian, only recently considered the death penalty for homosexuals.
The UN High Commissioner for Human Rights, Navi Pillay, said in a recent report that homosexuals and bisexuals face execution in at least five countries and 76 nations had laws criminalising gay sex, Reuters reported. They also accounted disproportionately for torture cases in jails around the globe.
Most African Christian churches remain sharply opposed to homosexuality, while the global Anglican Communion is in turmoil over the issue. Traditionalists are strongly opposed to the ordination of gay clergy and the blessing of same-sex relationships, whereas liberals have been urging tolerance and change.