In Tanhuato, 42 suspected criminals died in a reported shootout and one federal police officer was killed. In Apatzingan, eight civilians were shot dead in the street, some huddled together beneath an SUV for protection.
Human Rights Watch cited witness statements in the two confrontations.
"Based on the available evidence, it appears we're looking at two more major atrocities by Mexican security forces," said Daniel Wilkinson, managing director of the Americas Division at Human Rights Watch. "While the government insists that police acted appropriately in both cases, what witnesses describe clearly involves extra-judicial killings."
The Mexican government has categorically denied extra-judicial killings in either case, saying federal police responded after coming under fire.
In a visit earlier this month, the Inter-American Commission on Human Rights said Mexico is experiencing a "serious human rights crisis" and urged the country to investigate the same two incidents. Though it has not done a separate probe, the commission said there were irregularities in the government's investigations and that the crime scenes had been altered to support the official claims of a confrontation.
In the Apatzingan case, witnesses told The Associated Press at the time that the dead were former self-defense group members who were protesting that federal police had arrested 44 of their comrades, and that the protesters were armed only with sticks. Those who died came out of their trucks shouting that they were unarmed, witnesses told the AP.
Human Rights Watch said it interviewed a 19-year-old man wounded in the attack who said that two of the victims were shot in the head as they lay on the ground. The organization said two other witnesses corroborated the account. It did not name the witnesses.
In the Tanhuato shooting, a human rights official not with the organization interviewed three surviving witnesses, who said police shot people fleeing the scene or who had already surrendered. Human Rights Watch said it is protecting the identity of the official and the witnesses.
The two cases are reminiscent of a June 2014 massacre in Mexico State where the army said 22 alleged gang members were killed in a shootout that injured one soldier. An AP investigation at the scene indicated that the dead were lined up and shot against a wall.
While the government and the army initially denied the extra-judicial killings, a witness later came forward to say most of the dead were shot after they had surrendered. The government charged seven soldiers in the case, but four were released earlier this month for lack of evidence.
In another human rights case, the Inter-American Commission on Human Rights on Wednesday extended the mandate of a group of international experts who have been reviewing the Mexican government's investigation of the disappearance of 43 students in the city of Iguala in September 2014.
The Mexican government announced last week it would relaunch its investigation. The families of the missing students have refused to accept the government's version that their sons were killed and incinerated beyond recognition.
The experts released a scathing critique of the government's investigation in September. In part, they said it was impossible that the students were burned at a dump as the government had maintained. The government said it would take those criticisms into account in the new investigation.
The Associated Press