Defense attorneys for former Theranos CEO Elizabeth Holmes and Ramesh "Sunny" Balwani criticized prosecutors Wednesday for stalling to turn over what they call key documents that would clear their clients.

"The evidence produced so far confirms our belief that certain documents directly contradict allegations in the indictment," Lance Wade, an attorney for Holmes, told the judge. "While this information is comforting in a sense, it's startling that it wasn't gathered by the government."

Holmes and Balwani argue documents from U.S. agencies including the Food and Drug Administration and the Centers for Medicare and Medicaid Services are crucial in rebutting charges that they knew Theranos blood tests were inaccurate and misrepresented capabilities to investors, doctors and patients.

Defense attorneys pressed U.S. District Judge Edward Davila to get the government involved in producing these agency documents and said they've received about 20% of the documents they requested.

"The quickest way to fix this issue is to require the government to oversee the process," said Jeffrey Coopersmith, an attorney for Balwani. "I'm sure Mr. Bostick (Assistant U.S. Attorney) would have drafted his indictment differently if he has seen these documents."

But the prosecution said the defense misunderstands their position with the agencies.

"If this is about the government's access to the documents, the defense is getting the benefit of a higher level of information and more transparency than the government received," said Bostick.

Holmes and co-defendant Balwani are charged with nine counts of wire fraud and two counts of conspiracy to commit wire fraud with the now-defunct blood-testing company.

The charges portray a scheme by Holmes and Balwani to lie about Theranos' technology and dupe investor's out of hundreds of millions of dollars.

They each face up to 20 years in prison if convicted.

After hearing an hour of arguments on both sides Judge Davila set November 4 as the next hearing date.

Holmes ignored questions from CNBC as she left court on Wednesday.