The IRS acknowledged last week employees in its Cincinnati field office singled out conservative groups for extra scrutiny while evaluating applications for tax-exempt status.
Appearing on "Fox News Sunday," Ryan said he doesn't know why IRS officials did not tell Congress about the problem when they learned of it May 2012.
"I'm not necessarily going to speculate," he said. "We're going to investigate and find the answer to that question."
Ryan said it is clear the IRS "was targeting Americans based upon their political beliefs" for two years and that "the IRS misled Congress."
He said Congress will "get to the bottom of this -- who knew, what did they know, why did they do this, how high up in government did it go?"
"I mean, look, we have -- people have no trust that their government is being impartial," Ryan said. "This is arrogance of power, abuse of power to the nth degree, and we're going to get to the bottom of this."
Ryan -- the Republican nominee for vice president in 2012 -- said the administration bears "the burden of proof" to explain its handling of the September 2012 attack on a U.S. mission in Benghazi, Libya.
He declined to accuse President Barack Obama of downplaying the role of al-Qaida role in the attack to bolster his re-election chances, but he said the White House perpetuated a story "they knew was not true" about who carried out the attack and what motivated it.
"Why did they continue to perpetuate this story, which they knew was not true, and what was the reason for doing so?," Ryan said.
Senior White House adviser Dan Pfeiffer told Fox the primary goal of the administration at the time was to get all of the facts straight in a rapidly changing situation, in part to avoid making statements that might taint the investigation and impeded the search for the attackers.