The Corrupt Practices Investigation Bureau (CPIB), in a statement, said Iswaran, who was arrested in July last year, is alleged to have obtained kickbacks valued at S$384,340.98 ($286,181) from property tycoon Ong Beng Seng, partly to advance Ong's business interests.
Charge sheets show the favours include tickets to football matches, musicals, flights on Ong's private plane and tickets to the Singapore Formula 1 Grand Prix. Iswaran was advisor to the Grand Prix's steering committee, while Ong owns the rights to the race.
The CPIB said Iswaran faces a total of 27 charges, including corruption and obstructing the course of justice.
In his resignation letter, published by the prime minister's office, Iswaran said he rejected the charges and "will now focus on clearing my name". If convicted of corruption, he could be fined up to S$100,000 or face seven years in prison.
There was no immediate response to emails seeking comment from Ong's office. The property tycoon was also arrested in July as part of the corruption probe. Ong has not been charged.
The case has gripped Singapore, a major Asian financial hub that prides itself on a squeaky clean government that is rarely affected by graft and scandals involving political leaders.
Civil servants are highly paid to discourage corruption, with many cabinet ministers' annual salaries exceeding S$1 million.
In 2022, Transparency International ranked the city-state the fifth least corrupt country in its International Corruption Perceptions Index of 180 nations.
Iswaran, 61, joined Prime Minister Lee Hsien Loong's cabinet as a junior minister in 2006 and held trade and communications portfolios before becoming transport minister in May 2021.
The last corruption case involving a minister was in 1986 when the national development minister was probed for allegedly accepting bribes. The minister died before he could be charged in court.
Singapore is due to hold elections by 2025. In August, Lee admitted his ruling People's Action Party (PAP) had taken a hit over the graft probe and the resignations of two senior PAP lawmakers on account of an "inappropriate relationship".
The party is also due for a leadership transition with Lee promising to hand the baton to his successor Deputy Prime Minister Lawrence Wong by November.
Referring to Iswaran's case at a PAP event in November, Lee said the party must "show Singaporeans and the world that after half a century in government, the PAP’s standards remain as high as ever."
