K.P. Mohan of the Tamil-language Thinakkural daily was attacked as he walked out of Colombo's main hospital, where he had finished treatment for injuries suffered when soldiers beat him up in June, the Free Media Movement (FMM) said.
"The FMM expresses it serious concern at the continuing violence directed against journalists and the media in the country," the group said in a statement.
"This acid attack on Mohan is not only a threat to him but will make all journalists think twice before any critical reporting," it said.
Sri Lankan authorities are already investigating the June attack by air force personnel that happened on a travel route used by the country's air force chief.
There was no immediate reaction from the government to what is believed to be the first time acid was thrown at a reporter in the country, where journalist killings are regularly chronicled.
International media rights activists in June described Sri Lanka as one of the most dangerous places in the wor