Both cybersecurity and customer service at the Internal Revenue Service have suffered because of Obamacare, the agency's head said in remarks to Congress on Thursday.

"Congress, as I noted in my testimony, has underfunded … the Affordable Care Act," IRS Commissioner John Koskinen told a panel of the House Appropriations Committee. "That does not remove the statutory mandate we have that we have to implement the act."

Koskinen delivered his remarks in response to a question from Chairman Rep. Hal Rogers, R-Ky., who pointed out that Congress had "increased funding specifically for taxpayer services" in 2014 and 2016.

Koskinen said it didn't matter where Congress intended the money to go, explaining the agency had pulled funding for customer service and cybersecurity in order to ensure compliance with the ACA.

"As I said two years ago, at the continued level of underfunding, the things that were going to suffer were going to be enforcement, taxpayer service, and ultimately … information technology," Koskinen said.

More than eight million phone calls to the agency's customer service line went unanswered in the last filing season. Koskinen added that the agency hasn't fully funded customer service for the last "three or four years," and that about $900 million had been pulled from cybersecurity.