Miriam Rodriguez Martinez was shot in her home in the town of San Fernando in Tamaulipas state.
She was known for successfully investigating the kidnap and murder of her daughter by a local drug cartel, the Zetas.
The information she gave the police ensured the gang members were jailed.
But in March one of them escaped and her colleagues said she started to receive threats.
Her colleagues said she had asked for police protection but was ignored.
The Mexican human rights commission issued a statement saying it deplored her murder and called for a full investigation.
Mrs Rodriguez founded the local collective in her town for families who were victims of violence after her daughter was kidnapped in 2012.
She had managed to find her daughter's body in a clandestine grave and put her murderers in jail.
She also foiled an attempted kidnapping by the Zetas of her husband, when she chased the gang in her car, at the same time notifying the army who then managed to arrest them.
Frustrated by a lack of government help, groups of families began their own searches for people who had disappeared in their areas, taking courses in forensic anthropology, archaeology, law, buying caving equipment and becoming experts in identifying graves and bones.
There are now at least 13 of these groups across the country.
The administration of former President Felipe Calderon (2006-2012) militarised the Mexican security forces to fight the drug cartels.
In 10 years, the so-called war on drugs he launched left tens of thousands of murder victims with numbers varying widely between civic institutions and government figures.
The International Institute for Strategic Studies (IISS) issued its annual survey of armed conflict on Tuesday, saying that 23,000 people had died in Mexico in armed conflict in 2016
The Mexican government has questioned these figures.
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