The Association of Christian Financial Advisers (ACFA) says extending marriage "beyond its traditional boundaries" could create confusion for pension trustees and advisers.
Equalising marriage laws to permit same-sex couples to tie the knot would add to the already-complex regulations governing pensions, the ACFA said.
The House of Commons last night voted to allow gay marriage in England and Wales, even though 161 MPs, many of them Tories, opposed the government's plans.
The Marriage (Same Sex Couples) Bill now goes before the House of Lords.
"[The] ACFA is calling on the government to consider the significant financial implications of extending marriage beyond its traditional boundaries, based on principles of Judeo-Christian law," said the ACFA's Arwyn Bailey.
The ACFA said that, as the law stands, entitlements to pension benefits are less for those in civil partnerships than for married couples. Though some are calling for the law to be equalised by allowing same sex couples to marry, the ACFA said "equality cuts both ways" and that heterosexual couples would also need to be permitted the choice to enter into civil partnerships.
"And therein lies a problem," it added. "To change the law and apply it equally for all could create a serious conundrum for trustees of pension schemes."