Rappler, set up in 2012, is among a clutch of Philippine news organisations that have sparred with Duterte over their critical coverage of his drug war which the government says has claimed the lives of nearly 4,000 suspects.
Human rights groups charge that thousands more have been killed by shadowy vigilantes.
Duterte's spokesman said the president had decided to bar Rappler journalists from covering his events due to a "lack of trust".
"It could portend a broader assault on journalists and news organizations, whose critical watchdog role has magnified the government's poor human rights record," it said in a statement.
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The move came as the site also faced state-enforced closure, after the government's corporate regulator last month alleged that Rappler violated a constitutional ban on foreign ownership of local media.
Since taking power in 2016, Duterte has also publicly attacked other media outlets which have criticised his policies.
On Tuesday, guards barred Rappler's palace reporter from entering the grounds of the presidential office. She was later allowed to attend a news conference by Duterte's spokesman but prohibited from covering the president's speech.
The order came a day after the senate summoned Duterte's chief aide to answer questions following a Rappler report that he had intervened in a controversial $308 million frigate project by the Philippine navy. Duterte had branded the story as "fake news".
"She cannot have access to the president because the president is annoyed with her," Roque told radio DZMM, referring to the Rappler reporter who had defended the report during yesterday's briefing.
Rappler, which has appealed last month's ruling, decried Duterte's ban as an "attempt to intimidate independent journalists".
"It sends a clear and chilling signal that everyone else better report only what he wants you to or else," said the National Union of Journalists of the Philippines.