"I think most people would find it outrageous, and I think it's something that needs to be addressed and dealt with," Thune said on Fox News Channel's "On the Record with Greta Van Susteren" Monday.
Thune and Sen. Mark Begich (D-Alaska) spearheaded a letter last week signed by 60 senators that criticized the bonuses paid by the mortgage giants. The letter was sent to the Federal Housing Finance Agency (FHFA) and Treasury Secretary Timothy Geithner.
In the letter, the senators called on the FHFA to create a compensation structure that is more consistent with the agency’s mission.
The letter is a response to reports that 10 executives at Fannie and Freddie received a total of $12.79 million in bonus pay.
"It just looks terribly inconsistent, and I think it is, it is an outrage. You just got to show a little bit more of an ear about what's going on in this country right now," Thune said.
Thune also said he believes President Obama should get involved.
"This is something that has happened on his watch. He was very critical of Freddie Mac and Fannie Mae when he was running for office and the types of pay that was made to some of their senior officials," Thune said.
Fannie and Freddie have been receiving government support since September 2008, when they were brought under federal conservatorship. They have received about $141 billion in government funds so far.