Alfrery Líctor Cruz Canseco was shot on Sunday as he was waiting in his car after the church service had finished.
According to Christian human rights organisation CSW, his attacker attempted to escape, but was prevented from doing so by members of the congregation and was handed over to the authorities.
Pastor Cruz Canseco from Fraternidad Cristiana Church in the municipality of Tlalixtac de Cabrera is reported to have died from his injuries on the way to hospital.
The motive for the killing is unknown but follows a series of violent attacks against religious leaders in the country, including the disappearance of Pastor Aarón Méndez Ruiz on 3rd August.
CSW's Chief Executive Mervyn Thomas said: "The fact that he was targeted while in the pulpit is particularly shocking. We also remain concerned for the wellbeing of Pastor Méndez Ruiz and urge the Mexican government to spare no effort in ensuring his safe return, investigating all of these crimes and prosecuting those responsible."
The charity has called for the Mexican government to develop strategies to support all religious leaders who are under threat as "many criminal groups view church leaders and their influence as a threat to their power."
Thomas added: "The government must recognise the role that religious leaders play, not only as leaders of their churches, but also as voices for peace, justice and integrity, and human rights defenders, and afford them greater protection."
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