Valdez's murder came less than two weeks after a CPJ delegation met in Mexico City with Pena Nieto and other top government officials, and about a month after the killing of veteran reporter Maximino Rodriguez Palacios in La Paz on the Baja California peninsula.
Javier Valdez was killed when assailants opened fire on his vehicle in the state capital, Culiacan, according to RioDoce, the media outlet he co-founded and where he worked.
"Javier's murder is an attack on independent journalism not just in Sinaloa, but in Mexico as a whole", said CPJ's Mexico representative Jan-Albert Hootsen.
"Even though you may have bullet-proofing and bodyguards, [the gangs] will decide what day they are going to kill you".
Valdez also contributed dispatches to the national daily La Jornada and published a book a year ago about the dangers facing journalists who report honestly on the rampant crime and corruption gripping Mexico.
He had written about the Sinaloa drug cartel and its now-detained founder Joaquin "El Chapo" Guzman.
"Being a journalist is like being on a black list", Valdez said at a launch of his last book about drug gangs.
An award-winning local journalist and Agence France-Presse contributor who reported on violent drug gangs in Mexico was shot dead in the street Monday, a court source told AFP.
Journalists targeted in Mexico are most often local reporters in places where the rule of law is tenuous, but there have also been killings of journalists with national profiles such as Valdez and Regina Martinez Perez, who was slain in 2012.
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"The better you do journalism and the more passionate you are about it, the more alone you end up", he told La Jornada in an interview.
"The Committee to Protect Journalists honoured Javier Valdez Cárdenas with an International Press Freedom Award in 2011 to recognise his bravery and uncompromising journalism in the face of threats", said CPJ Executive Director Joel Simon.
He compiled much of his reporting into several books, the most recent of which, Narcoperiodismo, was published late previous year.
He also published titles about women's and children's experiences of drug violence.
Valdez is at least the sixth journalist to be murdered in Mexico since early March. Last year, 11 journalists were killed there overall.
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