Florida is experimenting a with an an innovative new funding scheme for schools.

And, it turns out that one of its “honors universities” doesn’t quite meet a key ranking requirement.

It has been ranked in the top five best value liberal arts colleges and one of the best public liberal arts universities by well-respected college ranking institutions. But a new performance ranking system in Florida for public universities may mean New College of Florida (NCF) will miss out on millions of dollars of state funding because it ranks low by the new criteria.

Located in Sarasota, Fla., New College is a small liberal arts university that focuses on independent research and collaboration rather than credit hours and GPAs. It is designated by the Florida legislature as the state’s honors liberal arts college.

However, a new Florida state funding system focuses on a university’s ability to prepare its students for the workforce, and New College is failing that grade. It is one of three state schools that fell below the required standards and will not receive any of the $100 million the state is allocating to public universities. The other two are the University of West Florida in Pensacola and Florida Atlantic University in Boca Raton.

The low grade means it may not receive any new funds and could see its annual budget slashed. For a small school of just under 800 undergraduates and some 75 research and instructional faculty members, that money will be a major loss.

The three low scoring universities are set to lose 1.0 percent of their base budget because of their ranking this year. But lawmakers want that to eventually go to 5.0 percent of their base budget in order to ensure universities take the standards seriously.

The new ranking system judges the universities on 10 different criteria, such as whether students go to graduate school or are employed full time within a year of graduation, starting salaries, and average cost of the undergraduate degree. The Florida Board of Governors, which oversees the state’s public universities, decided on the system earlier this year.

The Performance Funding Model Overview breaks down how each of the universities scored. New College, which is known to be an honors college for Florida, with its incoming freshman class having an average GPA of 3.92, was disappointed by its low grade but not surprised.

Media Relations Coordinator for New College David Gulliver told FoxNews.com in an email interview that New College was aware of the criteria that would be used in the ranking system. “We were aware of the metrics as they were being developed, and realized that some of them would not accurately reflect New College’s strengths,” said Gulliver.

The system does not track students who leave the state for work and it does not count students who go overseas for graduate school. Gulliver said that because the metrics only look at students who go to graduate school within a year after graduation, it misses the large number of students who go on to get graduate degrees within five years.