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.

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"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.

The agency has been hit with at least two successful cyberattacks in the past year. A cyberattack last year resulted in the theft of data on 330,000 taxpayers from the agency's "Get Transcript" database, while an attack last week resulted in the loss of special personal identification numbers associated with 101,000.

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President Obama's budget proposal for fiscal 2017 would increase funding for the IRS from $10.9 billion in 2016 to $12.2 billion in 2017, an increase of about 12 percent.