From January 1 2009, every cigarette on sale will come with the letters "SDPC" stamped near the filter, Singapore Customs said in a statement monitored on its website on Thursday.
SDPC stands for Singapore Duty-Paid Cigarettes.
"All unmarked cigarettes will be deemed to be duty-unpaid and illegal," the statement said.
Anyone caught with an unmarked cigarette will be committing an offence and will face a fine of 500 Singapore dollars (352 US) for every packet found in their possession, it said.
Travellers who bought cigarettes overseas for their own consumption should keep their receipts, it added.
The move to enforce the special marking also ties in with efforts to discourage smoking, it said.
"The availability of cheap duty-unpaid cigarettes will hamper our national effort to discourage smoking," said Fong Yong Kian, director-general of Singapore Customs.
"The marking will serve as deterrence against the peddling and buying of contraband cigarettes and help our officers in the enforcement efforts."
Branded cigarettes cost an average of more than 11 Singapore dollars a packet, making them among the most expensive in Asia, due mainly to the high duties aimed at discouraging smoking.
Singapore has some of the toughest anti-smoking measures in place, with bans on tobacco advertisements and laws to prohibit smokers from lighting up in entertainment outlets including pubs and nightclubs.
The Straits Times said Thursday that 2.1 million packets of contraband cigarettes were seized in the first seven months of the year, involving 16.2 million Singapore dollars in lost revenue for the government.
Last year, 32.9 million such packets were seized resulting in 32.9 million Singapore dollars in lost revenues, the newspaper said.