In the note, placed at Judaism's holiest site, Obama asks God to guide him and guard his family.
"Lord - Protect my family and me," reads the note published in the Maariv daily. "Forgive me my sins, and help me guard against pride and despair. Give me the wisdom to do what is right and just. And make me an instrument of your will."
Maariv published a photograph of the note on its front page on Friday. It said the note was removed from the wall by a student at a Jewish seminary immediately after Obama left.
The paper's decision to make the note public immediately drew fire from religious authorities. The rabbi in charge of the Western Wall, Shmuel Rabinovitz, said publishing the note intruded in Obama's intimate relationship with God.
"The notes placed between the stones of the Western Wall are between a person and his maker. It is forbidden to read them or make any use of them," he told Army Radio. The publication "damages the Western Wall and damages the personal, deep part of every one of us that we keep to ourselves," he said.
Many visitors to the 2,000-year-old Western Wall leave notes in its crevices bearing requests and prayers. Obama did so during a pre-dawn visit there Thursday, following a day spent meeting Israeli and Palestinian leaders. Obama bowed his head in worship after placing his small note of prayer into the wall.
The Western Wall is the lone remaining outer retaining wall of the second biblical Jewish temple, which was destroyed by the Romans in 70 A.D., and is revered at Judaism's holiest site. It stands where the bible says King Solomon built the first Jewish Temple, which was destroyed by the Babylonians in 586 B.C.
"It's inappropriate that the prayers of a person at the Western Wall should become a subject of public knowledge at all," said Jonathan Rosenblum, a Jerusalem-based analyst of the religious community and director of the Orthodox Am Ehad think-tank. "There is a rabbinic prohibition against reading other people's private communications and certainly anyone who goes to the wall expects that those communication will be protected."
Another Israeli paper, Yediot Ahronot, published an article Friday saying it had also obtained the note but decided not to publish it to respect Obama's privacy. Nearly all other Israeli media outlets ignored the story.
Thousands of notes and prayers are stuffed into the cracks of the wall. In recent years, The Western Wall Heritage Foundation, which operates the site, has opened a fax hot line and a Web site where people overseas can send their prayers and have them printed out and placed in the wall.
The wall is emptied of its notes several times a year. These are treated as a prayer book and buried, rather than burned.
Rosenblum said the Maariv publication showed "a lack of sensitivity," toward Obama and the wall. However, the extraction and publishing of the note do not appear to be illegal. Police said Friday it was not investigating the incident.
Obama spokesman Robert Gibbs would neither confirm nor deny the note was Obama's
The handwriting appeared to match a message Obama inscribed Wednesday in the guest book at Yad Vashem, Israel's official Holocaust memorial, and was written on stationery from the King David Hotel, where Obama stayed while in Israel.
Obama signed the Yad Vashem message. The note from the Western Wall was unsigned.
At the Western Wall, Obama was greeted by a crowd of curious onlookers and photographers. He donned a white skullcap, listened to a rabbi read a prayer, and inserted a folded white piece of paper between the stones. One hardline Israeli protester shouted, "Obama, Jerusalem is not for sale."
The visit to Israel and the Palestinian territories was part of an international tour meant to shore up Obama's foreign affairs credentials ahead of the November election. Obama's prospective rival, John McCain, visited Israel in March.