Philippines news website Rappler and its chief executive have been indicted on tax evasion charges, the latest in a case that free speech and civil liberties advocates have warned is part of a wider crackdown on dissent by President Rodrigo Duterte's administration.

Rappler said five cases were formally filed against Ressa and Rappler Holdings in two courts, just weeks after the Philippines Department of Justice announced it had found probable cause to indict the pair.

Philippines officials say some of the charges stem from Rappler and Ressa failing to declare about $3 million in 2015 on tax returns from an investment by the Omidyar Network, a fund created by eBay founder and philanthropist Pierre Omidyar.