The letters were sent to the Salt Lake City headquarters of the church, where powder spilled on a mail clerk's hand, and to a temple in Los Angeles. Both packages tested nontoxic, the FBI said Friday.
The two temples were sites of recent protests against the church's support for a California ballot initiative that superseded a court decision allowing gay marriage. The Mormon church, whose official name is the Church of Jesus Christ of Latter-day Saints, said it is stepping up security.
"We call upon those who have honest disagreements on this issue to urge restraint upon the extreme actions of a few," church President Thomas S. Monson said in a statement.
The Utah Pride Center, a gay rights group, put out its own statement calling the powder hoaxes and acts of vandalism "deplorable."
However, the group said, "It is false to conclude that yesterday's suspicious package came from gay protesters. Overwhelmingly, gay and allied Utahns have expressed their pain, frustration and commitment to securing rights through peaceful demonstrations and marches."
The coalition that ran the campaign to defeat Proposition 8 also issued a condemnation Friday.
"The NO on 8 campaign was about civil rights and seeking equality for all Californians. We have said time and again that the Mormon church deserves the same respect as any other religion," said Ali Bay, a spokeswoman for Equality California, the state's largest gay rights group.
The FBI is still investigating both cases, spokesman Juan T. Becerra said, noting that it's a crime to release a substance to threaten harm and stoke public fear.
"Even if you send a hoax threat, you're still in violation of federal law," Becerra said.
Anthrax mailed as a white powder to lawmakers and media members killed five people and sickened 17 in 2001. Since then, hoaxes modeled on the anthrax mailings have popped up but usually turn out to be harmless.
Separately, the coalition of religious groups behind the successful measure held a news conference to denounce protests carried out since Election Day.
The backlash has included calls for a boycott of Utah ski resorts and California businesses whose owners donated to the cause.