Perry said that it's a hard case, and told jurors to ask for more instructions if they need to.
The jury of six men and six women have been deliberating for almost three weeks.
Defendants Howard K. Stern and Drs. Sandeep Kapoor and Khristine Eroshevich are accused of conspiring to provide the Playboy model with excessive amounts of prescription drugs.
The three defendants are not charged in Smith's 2007 death, which was ruled as an accidental drug overdose.
The other question revolves around the complexities of a multi-faceted 21-count case. The verdict form is 42 pages.
Jurors asked if one were to believe that prescriptions were written in excessive amounts --- a violation of the business and professions code -- would it follow that those prescriptions also have no medical purpose, which is a separate violation of the health and safety code.
Perry said each charge must be considered separately.
The judge also urged the panel to reread parts of their jury instructions.
The defendants have argued for 10 weeks that they had been trying to relieve Smith's legitimate pain.
The prosecution alleges they went overboard to stay close to a beautiful celebrity.
The Associated Press Contributed to this report.