The Daily News of New York and ProPublica — a web-based platform specializing in investigative journalism — won the prize for public service journalism for coverage of New York police abuses that forced mostly poor minorities from their homes, Reuters reported.
Other winners included an international consortium of more than 300 reporters on six continents that exposed the so-called Panama Papers detailing the hidden infrastructure and global scale of offshore tax havens used by the high and mighty.
The Pulitzers, the most prestigious honors in American journalism, have been awarded since 1917, often going to famed publications such as The New York Times, The Washington Post and The Wall Street Journal.
However, they are also won by smaller, lesser known publications across the country whose work does not always gain national attention when it is published.
Reporter Eric Eyre of Charleston Gazette-Mail in West Virginia took the prize for investigative reporting for exposing a flood of opioids in depressed West Virginia counties with the country's highest overdose death rates.
The staff of the East Bay Times of Oakland, California, won the breaking news award for coverage of the 'Ghost Ship' fire that killed 36 people at a warehouse party, exposing the city's failure to take actions that might have prevented the disaster.
While the Pulitzer ceremony highlighted the news media's importance to democracy, it has been challenged by so-called fake news, which once referred to fabricated stories meant to influence the US election but has become a term used by Trump to dismiss factual reporting that is critical. Trump has frequently excoriated the media and in February called it "the enemy of the American people".
Operating in the glare of the 2016 presidential campaign, David Fahrenthold of The Washington Post took the national reporting award. The judges said he "created a model for transparent journalism in political campaign coverage while casting doubt on Donald Trump's assertions of generosity toward charities".
Fahrenthold found that Trump's charitable giving had not always matched his public statements. He also broke perhaps the biggest scoop of the campaign, revealing Trump had been captured on videotape making crude remarks about women.
The Wall Street Journal columnist Peggy Noonan, a longtime Republican, took the commentary prize for a series of critical pieces about Trump during the real estate magnate's successful run for the White House.
Reuters was a finalist in the national reporting and breaking news photography categories. Photographer Jonathan Bachman was recognized for his image of a woman being detained by police during a protest in Baton Rouge, Louisiana.
The 19-member Pulitzer board is made up of past winners and other distinguished journalists and academics. It chose the winners with the help of 102 jurors.
More than 2,500 entries were submitted this year, competing for 21 prizes. Seven of the awards recognize fiction, drama, history, biographies, poetry, general nonfiction and music.
The Pulitzers began in 1917 after a bequest from newspaper publisher Joseph Pulitzer.