The 787, operated by Japan Airlines was turned around shortly after leaving Tokyo's Haneda airport at 1:30 am (1630 GMT), a spokesman said.
"Several minutes into the flight, a message came on in the cockpit indicating a glitch with the anti-icing system for the left engine," he said.
"The glitch could not be sorted out quickly. The pilot expected some cloud and other elements en route to Singapore that could cause ice to form. So the decision was made to return to Haneda."
All but two of the 155 passengers on board opted to take the replacement Dreamliner offered, which left Haneda five hours later, the spokesman said.
The incident comes only weeks after JAL and All Nippon Airways (ANA), the single biggest operator of 787s, put their full fleets of Dreamliners back into service following a four-month suspension over battery problems.
A global grounding order was issued in January after lithium-ion batteries overheated on two different planes, with one of them catching fire while the aircraft was parked.
Boeing admitted in April that despite months of testing it did not know the root cause of the problems, but rolled out modifications it said would ensure the issue did not recur.
The JAL spokesman stressed that the latest incident did not affect the battery system.
"We are investigating the cause of the trouble," he added.
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