According to reports, he got off from his auto near a bridge across the river Nethravathi near Mangalore, about 375 KMs from Bengaluru, but did not return even after an hour.
Earlier in the letter he requests to continue running the business with a new management.
Coffee Day Enterprises said directors had discussed a letter to the board purportedly signed by the 57-year-old chairman in which he admitted mistakes handling his affairs. It is based on the unearthing of a credible evidence of financial transactions done by the CCD in a concealed manner.
Search teams have been looking in the Nethravathi river close to where the tycoon disappeared.
Coffee Day shares slumped by the 20% percent limit in Mumbai amid concerns about the company's future.
"The law should hold me and only me accountable, as I have withheld this information from everybody including my family".
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It was recently reported that Coca-Cola was in talks to purchase a large stake in the company, although this was not confirmed. Shares of Sical Logistics, another Siddhartha-promoted company saw its shares plunge 20 per cent to Rs 72.8 levels on the BSE in intra-day trade.
"We are deeply saddened by the developments and our thoughts are with his family at this time", KKR spokesperson said by email.
Siddhartha started his beverage empire in 1996 and was estimated to be worth $1.2 billion in 2015, Forbes reported.
Siddhartha founded Coffee Day in 1993 and opened the first Café Coffee Day in the tech center of Bangalore three years later. The company said it would "ensure continuity of business" in Siddhartha's absence.
Mr Siddhartha's offices were raided by income tax officers in September 2017.
He also wrote what seems to be an apparent suicide letter to the company board and to Coffee Day employees, saying that he had "failed to create the right profitable business model" and that he was giving up due to pressure from investors, borrowers and after having been troubled by issues with the tax department.
Siddhartha is also the son-in-law of former Karnataka Chief Minister SM Krishna. "This was very unfair and has led to a serious liquidity crunch", Siddhartha has written in the letter. He alleged in the letter that there was a lot of harassment from the previous DG, Income Tax Department, in the form of attaching "our shares on two separate occasions to block our Mindtree deal and then taking possession of our Coffee Day shares, although revised returns have been filed by us".