Some media outlets had speculated that Cornyn could put off his vote over concerns about foreign donations to a foundation headed by the Democratic New York senator's husband, former President Bill Clinton.
Cornyn's Washington, D.C. office confirmed the reports Tuesday afternoon.
Democratic lawmakers had hoped to approve Obama's proposed cabinet of top advisers within hours or days of his inauguration, but Cornyn's objections could stall approval of Clinton by one or two days, some political observers say.
A spokesman for Cornyn told Regional News Service Tuesday that the Senate will debate the issue Wednesday and follow it with a roll-call vote.
According to reports, Cornyn last week sent Hillary Clinton a letter congratulating her on her nomination.
At the same time, Cornyn reiterated his belief that the foundation headed by her husband should refuse all pledges and donations from overseas sources should she become secretary of state.
In his inaugural address, President Obama promised that those who manage the publics' dollars must be held accountable and will conduct their business in the 'light of day.'
"For too long, a dark veil of secrecy has stood in the way of the federal government and the American people. I have and will continue to make it a top priority to draw back this veil and shed light on how the federal government conducts its business and uses taxpayer dollars," Cornyn said in a statement issued after the address.
Sen. Cornyn first introduced the United States Authorization and Sunset Commission Act, S.1731, in June 2007.
This legislation, if approved, would establish a commission to evaluate the effectiveness and efficiency of federal programs and agencies.
The eight-member, bipartisan commission would advise Congress on such programs; suggesting whether they should be terminated, streamlined, consolidated or reauthorized.
Cornyn said he was pleased to hear President Obama voice his commitment to this type of transparency, and believes his legislation will achieve this goal.
"I hope President Obama will support me in this endeavor, and I look forward to working with him to achieve our common goal of creating a more open government that serves the needs of the American people," Cornyn said.