The Sri Lankan External ministry said that the US embassy statement refers to incidents surrounding the cancellation of a training organised for Jaffna-based journalists on July 26.
"The basis for such training programmes to be funded through the US Embassy is unclear, particularly when the target group has been limited to one geographical region and ethnic group," the ministry said in a statement.
"The US embassy has denounced the rights of a group of protesters against the embassy funded project to the freedom of assembly and expression," it added.
The US embassy had expressed concern over a media workshop for Tamil journalists which came to be cancelled after a pro-government group had protested against it.