The commission's comments follow a protest last month by thousands of ethnic Indians against what they say are discriminatory policies by the Malaysian government in favour of the majority ethnic Malays.
The protest in Kuala Lumpur was broken up by police using tear gas and water cannon and several protest organisers have been arrested.
The Hindu Rights Action Task Force, the group which organised the rally, says an average of one Hindu temple is being demolished every three weeks.
In its comments on Thursday the US commission said it was "concerned" by recent Malaysian government actions against the ethnic Indian Hindu minority "curtailing their human rights, including the freedom of thought, conscience, and religion".
Michael Cromartie, the commission chairman, said "continued discrimination against members of the ethnic Indian Hindu minority, including the destruction of sacred places and images, only fuels religious unrest and intolerance".
The government says it does not target the Hindu community and its demolition of places of worship are because they are illegal structures or because land is needed for development.
It has also rejected accusations of discriminatory policies against ethnic Indians.
Abdullah Ahmad Badawi, the Malaysian prime minister, has accused ethnic Indian activists of stirring up racial conflict and threatened to use a law that allows for indefinite detention without trial.
In an opinion piece published on Friday in the Asian Wall Street Journal, Abdullah wrote that "the right to protest is fundamental, but it is a right that must be matched by a responsibility to respect general public safety".
While maintaining that he would listen to "all points of view and concerns that are honestly and reasonably presented", he said "we cannot and shall not tolerate those who seek to incite or provoke violence for their own personal gain".
The November 25 protest followed another rally on November 10 – also dispersed by force - to demand electoral reforms.
Together, they have presented the biggest challenge to Abdullah's authority ahead of elections which are expected to be called soon.