After speaking to Smith, stewards suspended the trainer after finding him guilty of giving false evidence and another charge of refusing to give evidence relating to unlabelled and unidentifiable substances in the stable.
Group One winners In Her Time and El Dorado Dreaming were transferred to Kris Lees who trains next door.
The winner of the ATC Sires' Produce Stakes, El Dorado Dreaming was withdrawn from Saturday's Tea Rose Stakes.
Stewards said on Monday, additional samples had been taken from El Dorado Dreaming and another horse which produced an irregularity with the results expected later this week.
The other four samples including that taken from In Her Time were satisfactory and those horses are allowed to race.
In Her Time is listed to run in a barrier trial at Newcastle on Wednesday before she resumes in the Premiere Stakes as her lead-in to the $13 million Everest on October 13.
Smith has applied for a stay of proceedings pending an appeal against his suspension but the Racing NSW Appeal Panel has not yet made a decision.