By R. Jai Krishna 

NEW DELHI--India's highest court Wednesday ordered Samsung Electronics chairman Lee Kun-Hee to come to India to face criminal charges in a case where a subsidiary is accused of failing to pay one of its suppliers.

The Supreme Court of India said Mr. Lee has six weeks to appear before a court in the city of Ghaziabad, in the northern state of Uttar Pradesh. After the deadline, police will have orders to arrest Mr. Lee if he enters India, the court said. The court has charged Mr. Lee of cheating, fraud and criminal conspiracy.

The transactions connected to the criminal charges facing the head of South Korea's largest conglomerate date back about a decade. A New Delhi-based company called JCE Consultancy is claiming that Samsung's Dubai subsidiary failed to pay it $1.43 million.

Samsung said its chairman, Mr. Lee, has no connection to the case, noting he isn't involved in the day-to-day operations of many overseas subsidiaries.

"There are no grounds, let alone evidence, to support the accusation against Chairman Lee," Samsung said.

In 2008, Mr. Lee resigned from Samsung amid a tax fraud scandal. He was eventually cleared of the charges but found guilty of breach-of-trust and tax evasion in 2009 and handed a suspended prison sentence.

The government later pardoned Mr. Lee and he returned to the company in 2010 and has had an active hand in the company's direction.

Mandeep Vinayak, a lawyer for JCE Consultancy said Samsung has refused to pay the money it owed, so JCE had to take the case to court.

Samsung is claiming it is also a victim, saying that the case in India is a remnant of a "fraud" where the money of its subsidiary--Samsung Gulf Electronics--was misused.

It wasn't immediately clear who was involved in the fraud at Samsung's Dubai subsidiary.

"We are confident that the Indian Courts will recognize the innocence of Chairman Lee and deliver justice," Samsung said in a statement.

Wednesday's order is the latest example of heavy-handed moves by Indian authorities on high-profile companies.

Several multinationals--including Vodafone Group PLC, Royal Dutch Shell PLC, Nokia Corp. as well as technology firms Google Inc. and Facebook Inc.--are involved in legal disputes in India.

"Unfortunately, it sends a very bad message and dampens the spirits while India is trying to boost foreign investments and investor sentiments," said Aparajit Bhattacharya, head of foreign investments and corporate deals at New Delhi-based law firm HSA Advocates.

As India is suffering one if its slowest stretches of growth in a decade, it has been hoping to attract more foreign investment.

However much of the excitement about the country's massive middle class has died down in the last two years, meaning fewer foreign firms are making big bets on the India opportunity.

While New Delhi has tried to loosen some restrictions on foreign investment in retail and other industries, hoping to jump start interest, global brands have become more cautious about expanding in the south Asian nation.

One of the reasons, say some executives and analysts, is concern about the country's overburdened and unpredictable court system.

"The rise in litigation is a negative for foreign investment in India," said R.K. Bhasin, joint director at Associated Chambers of Commerce and Industry, one of India's three largest trade groups. "The government needs to build proper checks and balances to reduce litigation."

Prasanta Sahu contributed to this article.

Write to R. Jai Krishna at krishna.jai@wsj.com

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