It comes after US aircraft regulators approved a revamped battery design.
Problems with the plane's battery had resulted in the entire fleet of the 787s being grounded and deliveries of the aircraft being halted.
Japan's All Nippon Airways and Japan Airlines are among the first carriers that will have the batteries replaced.
All Nippon Airways (ANA) and Japan Airlines (JAL) are the two biggest operators of the 787 Dreamliner.
"We began the work as we have received instructions from Boeing following the Federal Aviation Administration (FAA) approval," a spokesman for JAL said.
"But we have not decided on the timing of the 787 flight resumption."
Ryosei Nomura, a spokesman for ANA, said that the technicians had started installing new batteries on five of its 17 Dreamliner aircraft.
The carriers still have to wait for approval from various regulators before they can start to fly the planes commercially.
The FAA, which approved the battery design last week, has said that it will issue a final directive on the Dreamliner this week.
Other international regulators are likely to follow. but it may still be a couple of weeks before flights resume.
The plane is the first in the world to use the lithium-ion batteries, which are lighter, hold more power and recharge more quickly.
But after incidents in which some of the batteries emitted smoke, all of the 50 Boeing 787 planes in service were grounded in mid-January.
The problems sparked a battery fire on a parked JAL 787 at Boston's Logan International Airport and another incident in which battery smoke forced an emergency landing of an ANA 787 in Japan.
The grounding has cost Boeing an estimated $600m (Â£393m).
Japanese carrier ANA lost some 1.4bn yen ($15m; Â£9.5m) in revenue through January's disruption alone.
Boeing has started replacing batteries on some of its grounded 787 Dreamliner fleet, moving a step closer to getting the planes flying again.