Avigdor Lieberman filled in the top position for about an hour while Netanyahu, 64, underwent a routine gastrointestinal exam as part of his annual medical checkup, Ynetnews.com reported.
Netanyahu's office said he successfully underwent the examination during which a polyp was removed from his large intestine.
Netanyahu's personal physician, Dr. Zvi Herman Berkowitz, said recent medical exams indicated the prime minister was in good health.
Last Saturday Netanyahu was taken to a hospital after suffering from nasal problems and a severe headache. He was released a short time later.
In August, Netanyahu underwent a hernia operation.