"I will raise these issues directly with President Castro," said Obama.
The proposal includes the creation of a National Search System to coordinate the efforts of the Attorney General's Office (PGR) and the local prosecutors offices.
The discovery in the state of Morelos has raised questions about whether the case is another example of shoddy police work that denied families the right to recover the bodies of their loved ones, or something even more sinister.
Washington retired some of the funds for the Merida Initiative due to "concerns" on human rights.
The Ministry of the Navy denied any human rights violations.
UN high commissioner for human rights Zeid Raad al-Hussein said armies weren't designed for police work.
Francis also asserted that the world's poor have a right to education, lodging, labor and land.
According to the 2014 Human Rights report published by the Bureau of Democracy, Human Rights and Labor of the U.S. Department of State, prosecution for all forms of crime is extremely low in Mexico.