Shoemaker's attorneys on Monday filed a 36-page motion arguing to Senior U.S. District Judge Neal B. Biggers Jr. that the government didn't have enough evidence to support all the guilty verdicts.
They also claim some of his convictions constitute "double jeopardy" and aren't supported by enough evidence.
Shoemaker, 39, and co-defendant Batesville businessman Lee Garner, 67, were convicted March 2 in the scheme surrounding their dealings with Tri-Lakes Medical Center in Batesville, where Shoemaker was a top executive.
They face lengthy prison sentences and substantial fines. No date for sentencing is set.
The new motion also cites what defense attorneys claim is an erroneous instruction, which allowed the jury to convict Shoemaker if it found he "deliberately closed his eyes to what would otherwise have been obvious to him."
All counts of his September 2011 indictment charge him with acting knowingly and willfully, they say.
"This jury instruction effectively relieved the government of this burden of proof, permitting the jury to convict Shoemaker for acting carelessly or negligently."
Among other reasons, his counsel adds that because a 26-count indictment against the government's chief witness was not discovered until after they cross-examined him, they insist it constitutes "prosecutorial misconduct," which prevented them from fully questioning him.