The Judicial Service Commission (JSC) last week decided not to pursue a misconduct investigation against Hlophe.
The decision followed claims by two Constitutional Court judges last May that he approached them about the now abandoned corruption case against President Jacob Zuma.
Hlophe, who was on special leave while the matter was before the JSC, was expected to return to work on Monday.
However, his secretary said on Monday afternoon he "hasn't arrived yet".
She had no idea when he would come in.
Other court staff said they did not know whether Hlophe's deputy, Jeanette Traverso, was still acting judge president