Morales, D-Silver City, said the state Public Education Department's formula for grading 830 schools was capricious, volatile and inaccurate.
He said he spoke to Gov. Susana Martinez about his ideas for restructuring the system before introducing his bill hours before the filing deadline.
Martinez, a Republican, pushed hard in 2011 for the A-F system. In her first two years in office, grading schools was the most high-profile of her education initiatives to receive legislative approval.
Because Republicans and Democrats alike are concerned about a flawed grading system, Morales said, he hoped the governor would support a bill to rework how schools are evaluated.
Larry Behrens, a spokesman for the Public Education Department, had a tart response when asked about Morales' bill.
"We're always open to fine-tuning the A-F system. However, since the sponsor decided to simply introduce the bill instead of working in cooperation with PED first, we're skeptical of the intentions," Behrens said.
Morales, who has a doctorate in education, said school grades need to be built on more reliable statistics that would give teachers, principals and boards of education a blueprint of how to improve.
Last year, the principal of Santa Rosa Elementary School told legislators that the A-F system was a huge improvement over the pass-fail formula of the federal No Child Left Behind Act.
Its principal, Lee Vega, was happy when his school of 240 students got a B in the preliminary round of state grading in January 2012. But six months later, when the first binding state grades were issued, Santa Rosa Elementary dropped all the way to a D.
Morales and other legislators questioned how school grades could fluctuate so much in so short a time.
Another strike against the system occurred last summer when Paul Aguilar, deputy secretary of public education, appeared before a legislative committee. Aguilar said the A-F grading system was so complex that perhaps only five people in the state understood it.
Hanna Skandera, secretary-designate of public education, said in a subsequent interview that the A-F system was a significant advance for New Mexico and every part of it was explainable.
One of Morales' ideas is to end the grading curve that the Public Education Department uses. He said it pits schools in wealthier towns or neighborhoods against those at the opposite end of the income scale. The state's grading system tries to account for those disparities by recognizing gains or setbacks in student achievement.
Behrens said the state's A-F system was approved by national experts through the U.S. Department of Education.
"In fact, New Mexico's A-F system holds us accountable for over 20,000 students who were previously uncounted" in federal ratings, he said.
As evidence that Morales' criticisms were off base, Behrens pointed to the Data Quality Campaign, a nonpartisan Washington organization that advocates data use to improve student achievement.
"New Mexico's state report card provides clear explanations of the data included in the report by limiting its use of education buzzwords and defining the ones it uses. Most importantly, New Mexico's reports clarify why it looks at specific data sets and how it finds results," the organization said.
Morales' proposal to change the grading system is Senate Bill 587.