Menachem Mazuz issued the advisory in response to a high court petition demanding that Katsav resign following a police statement that there was evidence he had raped and sexually assaulted female employees.
Israel's justice ministry quoted Mazuz as telling the high court that due to the serious nature of the allegations Katsav should "consider suspending himself from duty by asking parliament to declare him temporarily incapacitated".
Katsav, 60, denies the allegations. His office declined comment.
Katsav had already absented himself from the swearing-in of the new high court president earlier this month.
The justice ministry is considering whether evidence compiled against Katsav warrants prosecution.
If it decides to pursue the case, it would be the first prosecution of an incumbent Israeli president on felony charges.
Mazuz, who has final say on whether to go to court, said a trial would require Katsav to stand down pending a verdict.
Once an indictment was served against Katsav, the justice ministry said "it would be against procedure and propriety for the president to continue in office".
The post of president is largely ceremonial in Israel, meaning the case is unlikely to have any direct effect on the government.