Moshe Katsav will be questioned on Wednesday about claims he sexually harassed two female former employees. One woman has also reportedly alleged that Katsav received money for granting pardons.
"There will be questioning going on," Mickey Rosenfeld, a police spokesman, said. "That's the first time that we will actually have contact ... It's all being done in co-ordination with him".
Katsav has denied any wrongdoing and his office has said he would co-operate with the investigation. "The president is interested in giving his full version and to prove the lies of the serious accusations," a statement said.
Computers and documents were confiscated by police during the raid on Monday night. Investigators are planning to review Katsav's e-mails and the pardons he has granted during his term, which began in 2000, an official said.
The Israeli president serves a single seven-year term and enjoys immunity from trial on charges related to their tenure in office, but they are not immune from investigation, according to the justice ministry.
Katsav, a longtime backbencher in the Likud Party, was elected to the presidency by parliament in a surprise win over Shimon Peres.
The position is largely ceremonial but the president is expected to set a high moral standard and help unify the country during times of trouble. During the recent conflict in Lebanon Katsav visited areas hit by rocket fire, rushing for shelter in a building during one barrage.
The Katsav investigation is the latest in a series of scandals to hit Israeli politics.
Sexual harassment allegations have already forced Haim Ramon, the justice minister, to resign. He is accused of improperly kissing an 18-year-old female soldier.
Tzahi Hanegbi, another prominent member of the Kadima party, was informed earlier this week he would be charged with fraud, bribery and perjury.
Dan Halutz, the head of Israel's armed forces, has come under fire for selling his stock portfolio just hours before the war and Ehud Olmert, the prime minister, is facing a possible investigation into a Jerusalem property deal.