Suresh Kalmadi, a lawmaker for the ruling Congress party, faces charges of criminal conspiracy, forgery, abuse of office and intimidation over a contract awarded to Swiss Timing, which is part of the Swatch luxury goods empire.
Swiss Timing, which is named in the case but has not responded to a court summons, won a 1.1 billion rupee ($21 million) contract to serve as the official time-keeper and results provider.
Kalmadi signed a statement to declare his innocence of all charges and did not address the court.
Agarwal said that Kalmadi may try to challenge the decision to order a trial in the High Court.
"We will examine the charges and take a further decision on the matter," the lawyer said.
Seven others on trial also pleaded not guilty in written statements submitted to a special court set up to try the suspects over the massively over-budget Delhi event.
They face a maximum sentence of life imprisonment.
Also facing charges are Kalmadi's deputy during the Commonwealth Games Lalit Bhanot, who has since been elected number two in the Indian Olympic Association in a scandal-tainted process.
The dysfunctional organization of the Delhi event — the most expensive in Commonwealth Games history at $6 billion — led to Kalmadi becoming a public hate-figure and he was booed by the crowd during the two-week event.
In the police charge sheet detailing their evidence against the accused, Swiss Timing is accused of paying money to companies as kickbacks to Kalmadi and others via its local partner Gem International.
In one instance, Gem is accused of paying a Hyderbad-based firm for cabling work at an inflated price.
The company allegedly had no previous experience and was unable to produce proper paperwork to investigators.
The Delhi Commonwealth Games were intended to showcase India on the global stage, but infrastructure problems, delays and widespread corruption allegations instead highlighted many of the problems that blight the country.
They also led to criticism of the stranglehold of politicians over Indian sports associations.
Kalmadi, an MP of more than 30 years who smiled at the press as he entered court in a grey suit, ran the Olympics body for 16 years.
The former air force pilot stepped down at the end of 2012 and was replaced by Abhey Singh Chautala, a local politician from the state of Haryana seen as a close ally of Kalmadi.
Bhanot was also elected unopposed as secretary-general of the Olympics body, which led the International Olympic Committee to suspend India because of the tainted nature of the leadership transition.
The Delhi Commonwealth Games organising committee's director-general V.K. Verma, procurement director Surjit Lal, sports director A.S.V. Prasad, treasurer M. Jayachandran and three others are also on trial.