Justice Secretary Guillermo Somoza said his office's special task force on hate crimes found there have been 23 murders of gays and transgender people since the fall of 2009, The Miami Herald reported.
The crime wave began in November 2009 when a transgender teen was decapitated, dismembered and set ablaze.
Gay and transgender people in Puerto Rico say it has become socially acceptable to despise them.
Francheska Gonzalez, a transsexual who suffered broken vertebrae and a ruptured right breast implant during an April beating, pointed to growing fundamentalist rhetoric as promoting hatred.
"A lot of church people are not teaching peace and to love thy neighbor," Gonzalez said. "They are teaching to hate gays."
Pedro Julio Serrano of the National Gay and Lesbian Task Force accused Puerto Rican Senate President Thomas Rivera Schatz of anti-gay rhetoric.
Schatz makes it a point at confirmation hearings to ask senior government job candidates whether they support gay marriage, Serrano said.