In a Thursday interview with CNBC's Jim Cramer, Fair Isaac CEO Will Lansing pushed back against recent criticism of his company, saying FICO credit score pricing isn't an issue for home owners.

"We have been accused of raising our prices, and it's true, we have, but they're still very, very small relative to what we offer," Lansing said. "We charge $4.95 for a mortgage score out of $6,000 in closing costs. So it's not the cost of a FICO score that's...creating problems for home ownership."

In May, Bill Pulte, the newly-appointed head of the Federal Housing Finance Agency, chastised Fair Isaac for its price hikes. Pulte later announced that mortgage lenders can now choose to use a traditional FICO score or one from rival VantageScore to evaluate borrowers. Previously, mortgage lenders selling loans to Fannie Mae and Freddie Mac — government-sponsored enterprises that back the majority of residential mortgages in the U.S. — were only allowed to use FICO scores. Pulte later went on to disparage Fair Isaac as a "monopoly who has ripped off Americans for decades."

FICO said in a statement that the new policy "introduces a dangerous precedent that increases adverse selection risk" and "inexplicably favors a less predictive credit score that will undermine the safety and soundness of the enterprises and their counterparties."

Lansing reiterated his company's statement, telling Cramer "there's all kinds of safety and soundness concerns" with the FHFA's actions.

According to Lansing, Fair Isaac has been competing with Vantage for 15 years and "we always win," touting the widespread use of the traditional FICO model. He also said Fair Isaac's new credit score model, FICO 10T, outperforms the classic model and that of VantageScore.

"We have over 90% market share in all these other markets that have nothing to do with the government," Lansing said. "And then within the mortgage market, in the non-conforming market where there's no government mandate, FICO is the clear industry standard."

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