The decision to return migrants fleeing an earthquake and political instability was "inhumane", senior diplomat Daniel Foote said in a damning letter.
Last weekend, the US started deportation flights from a Texas border town, where about 13,000 migrants had gathered under a bridge.
They have been waiting in a makeshift camp in temperatures of 37C.
Local officials have struggled to provide them with food and adequate sanitation.
Since Sunday, the US has returned to Haiti 1401 migrants from the Texas camp on the border with Mexico.