The letter, signed by officials from the Education and Justice departments, does not have the force of law but contains an implicit threat that schools which do not abide by the Obama administration's interpretation of the law could face lawsuits or a loss of federal aid.
The move comes in the wake of the controversy surrounding the so called bathroom law in North Carolina.
Because of the differences, the State of North Carolina and the federal government sued each other last week.
"No student should ever have to go through the experience of feeling unwelcome at school or on a college campus," said John B King Jr , Education Secretary.
"We must ensure that our young people know that whoever they are or wherever they come from, they have the opportunity to get a great education in an environment free from discrimination, harassment and violence," he said.
The letter going from the federal government is not a law but a directive to schools, the non-implementation of which might affect their federal funding.