The court also turned down an industry plea to stay the implementation of the new tobacco-control rules introduced from April 1, which require health warnings to cover 85 per cent of a cigarette pack's surface, up from 20 per cent earlier.
The tobacco industry "should not violate any rule prevailing as of today", the two-judge bench said during the 45-minute hearing inside a packed courtroom in New Delhi.
It also directed the high court of Karnataka state to hear dozens of pleas filed against the new rules in several Indian courts and decide on the matter within six weeks.
Last month, Indian tobacco companies, some backed by foreign "Big Tobacco", briefly shut down production as the new rules came into effect. The industry says the new policy is impractical and says it will boost cigarette smuggling.
But the government still backs the rules that are aimed at reducing tobacco consumption. Ranjit Kumar, solicitor general of India, told the court New Delhi was committed to the new rules and opposes any stay on their implementation.
The Supreme Court declined an industry lawyer's request that a stay obtained by a lower court be allowed to continue.
Shares in India's biggest cigarette maker ITC Ltd, part-owned by British American Tobacco, fell nearly 1 per cent after the court directive. US-based Philip Morris International's India partner Godfrey Phillips pared gains but was trading 1.3 per cent higher.
Officials from the Tobacco Institute of India, an industry lobby group whose members include ITC and Godfrey, were not immediately available for comment.
It was not immediately clear when the companies will start printing bigger warnings on their packs.
Smoking kills more than 1 million people a year in India, according to BMJ Global Health. The World Health Organization says tobacco-related diseases cost India $16 billion annually.
© Thomson Reuters 2016