The court ruled this week that Lee, South Korea's richest man with an estimated net worth of $11.2 billion, should appear before the trial court in Ghaziabad, on the outskirts of New Delhi, in the next six weeks.
Dating back to 2002, the case stems from a complaint by New Delhi-based JCE Consultancy accusing Samsung Electronics of "cheating" the Indian company out of $1.4 million by failing to honour a commitment to pay a bill.
"Chairman Lee has no relation to this case whatsoever," Samsung said in a statement.
"There are no grounds, let alone evidence, to support the accusation against chairman Lee," it said, adding that he was not involved in the day-to-day operations of Samsung's many overseas subsidiaries.
The statement declined to address the Indian Supreme Court's order for the 72-year-old to appear in person, and a Samsung spokesman declined to comment further on the matter.
Samsung said the case was related to a "multi-million dollar fraud scheme" perpetrated against a Samsung subsidiary in Dubai, Samsung Gulf Electronics.
"Samsung Gulf Electronics is a victim of this fraud scheme," it said.
"We are confident that the Indian Courts will recognise the innocence of Chairman Lee and deliver justice," it added.
Lee's lawyers had tried unsuccessfully to have the case thrown out of court in India.
In its ruling, the Supreme Court made no comment on the merits of the case, saying that was up to the trial court to decide.
Indian courts have a track record of summoning top executives who, despite having no direct involvement in alleged offences by their companies, are deemed to be potentially responsible because of their seniority in the firm.