The latest questioning of Kim Hyun-chul, 37, came amid indications that a four-month government investigation into the Hanbo Steel corruption case was nearing an end.
The president's son did not speak as he waded through an army of reporters asking questions before entering the prosecutor's office.
A 30-minute motorcade taking him from his home through downtown Seoul streets to the prosecutor's office was broadcast live by South Korea's national TV networks.
In February, Kim Hyun-chul, who is the president's second son, was questioned and cleared of any wrongdoing. But prosecutors reopened their investigation after critics called the initial probe a whitewash.
In April, testifying before a parliamentary hearing, Kim Hyun-chul tearfully claimed that he was poor and did not hide any money in any form.
But on Thursday, senior prosecutor Shim Jae-ryun told reporters, "We will prove piece by piece" that the son has taken bribes. "We expect him to deny the allegations at first, but he will eventually have to cooperate."
Prosecutors say they have evidence that from mid 1993 to late 1995 Kim Hyun-chul received billions of won (millions of dollars) from three companies, some as kickbacks in return for influence-peddling.
If found guilty of bribery, the president's son could be sentenced to up to five years in prison and a fine of up to $11,500.
Case grew out of steel company collapse
The scandal grew out of the bankruptcy of Hanbo Steel Industry Company in January.
Eleven people, including close aides to President Kim, ruling and opposition party lawmakers, a former cabinet minister, bankers and businessmen are on trial on charges of taking or giving bribes in exchange for arranging improper bank loans to Hanbo.
Opposition parties have identified the president's son as the main backer of the steel company, which collapsed after piling up $6 billion in debt.
Koreans feel betrayed
Many Koreans said they felt betrayed by yet another scandal following the imprisonment of former presidents Chun Doo-hwan and Roh Tae-woo for raising hundreds of millions of dollars in slush funds while in office.
"This is too much. Even President Kim Young-sam's son is no different from Chun and Roh," said saleswoman Kim Chum-soo who added that most of her clients wanted to see the president's son behind bars.
But few Koreans said they would like to see President Kim stepping down over his son's wrongdoing.
"The country is going through hard times. I wouldn't want to see more chaos with the president resigning," said Lee Byung-ok, a pastor.
President Kim's five-year single term ends next February. He is barred by the constitution from running again.
Reporter Lim Yon-suk and Reuters contributed to this report.