"As a result, there were no claims on any of National's insurance policies," it said in a statement.

The National Public Finance Guarantee Corporation—an indirect subsidiary of MBIA —separately confirmed Wednesday that the island's struggling power utility, Prepa, and other Puerto Rico-related institutions made their debt-service payments.

With the payments, the island, for the moment, avoided sinking further into financial crisis. Puerto Rico Gov. Alejandro Garcia Padilla recently called its roughly $73 billion in debt "not payable," fueling concerns among investors and bond insurers.

Debt-riddled Puerto Rico paid all of its $1.9 billion in obligations due on Wednesday, sources told CNBC.

National also noted it and other forbearing bond insurers would provide $128 million of short-term bridge financing to "strengthen Prepa's liquidity position while these vital negotiations continue." It said its Puerto Rico exposure decreased by about $250 million because of the payments.

Read MorePuerto Rico poses a 'significant risk': Strategist



"By honoring its legal obligations to bondholders, Prepa can return its full attention to addressing its operational and financial challenges," National added.

On Monday, Garcia Padilla called for restructuring and reforms, saying Puerto Rico seeks to reach a moratorium with bondholders and hold off on making some debt payments for "years." Puerto Rico's economic and fiscal situation has grown direr, and Garcia Padilla has repeatedly warned that the island may not generate enough income to meet its obligations.

Puerto Rico's government has attempted to cut costs amid the crisis. Garcia Padilla has said he would not consider cutting the minimum wage, among other potential cost-trimming measures.

Read More Insured Puerto Rico debt holders in 'good shape?'

This story is developing. Please check back for further updates.

for the latest on the markets.

—CNBC's Kate Kelly contributed to this report.