"We encourage Indonesia, which rightly prides itself on diversity and tolerance, to respect and uphold international rights and standards by ensuring equal rights and protections for all of its citizens," State Department spokeswoman Elizabeth Trudeau told reporters.
Earlier on Thursday, Indonesian presidential spokesman Johan Budi told AFP that "rights of citizens like going to school and getting an ID card are protected, but there is no room in Indonesia for the proliferation of the LGBT movement."
He was responding to criticism that officials recently unleashed a wave of angry rhetoric against Indonesia's lesbian, gay, bisexual, and transgender (LGBT) community.
Washington is "closely monitoring reports of possible measures in Indonesia that would restrict the freedom of expression for LGBTI individuals," Trudeau said.
"In principle and in practice the United States government will always strive to protect and advance the universal right of all people, including LGBTI individuals, to express themselves both online and offline," she added.
Indonesia's LGBT citizens have long been targeted by vigilante Islamist groups.
But the community experienced an "immediate deterioration" in their rights following a sustained assault by ministers, religious hardliners and influential Islamic organizations - including a call to ban them from university campuses - over a two-month period earlier this year, Human Rights Watch said in a report released Thursday.