Documents and computer equipment were seized from the Mossack Fonseca office, officials said on Twitter.
The attorney general's office said the Mossack Fonseca sign had been removed a day earlier and quoted an employee as saying the firm was moving.
The leak showed how some wealthy people use offshore companies to evade tax.
The raid was overseen by El Salvador's Attorney General Douglas Melendez.
Mossack Fonseca's El Salvador branch was able to provide "back office" functions for the firm's clients all over the world, according to a document posted on Twitter by the attorney general's office.
Local news website El Faro reported (in Spanish) that Salvadoreans had used Mossack Fonseca to buy property in the country without declaring  the purchases to the Salvadorean authorities.
The firm has denied it has done anything wrong and says the information is being presented out of context.
Elsewhere:
Authorities in El Salvador have raided the offices of the Panama law firm at the centre of a massive data leak, the attorney general's office says.