All Nippon Airways said it would begin test flights of its 787s on Sunday.
It also needs to fight off competition from emerging low-cost carriers and rival All Nippon Airways (ANA).
All Nippon Airways says 40, 000 seats have been cancelled on its China-Japan flights since the row began.
Meanwhile, an All Nippon Airways flight was forced to make an emergency landing because of a battery malfunction.
On Friday, All Nippon Airways reported a crack in the window on the pilot's side of the cockpit.
Nine days later a smoking battery aboard an All Nippon Airways 787 led to an emergency landing in Japan.
The first test flight in Japan was Sunday, All Nippon Airways officials said.
All Nippon Airways owns 17 of the jets and Japan Airlines has seven.
Last week, rival All Nippon Airways warned that it would take a 1.4bn yen hit from the Dreamliner grounding.
It comes after an All Nippon Airways (ANA) 787 had to make an emergency landing due to a battery malfunction.
Similarly, Singapore credits only 70% for miles flown on All Nippon Airways in economy class and nothing for certain discount tickets.
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Of the 50 Dreamliners delivered to date, 24 of them are being operated in Japan by JAL and rival All Nippon Airways.
Japan's All Nippon Airways has resumed commercial flights of the Boeing 787 Dreamliner for the first time since the planes were grounded over safety fears.
Yesterday a brake problem on a Dreamliner forced authorities to cancel an All Nippon Airways flight at Yamaguchi Ube Airport in Japan.
The biggest is Star, built around Lufthansa, United and All Nippon Airways.
Similarly, All Nippon Airways, the country's biggest domestic airline, has said that it wants to reduce investment and get rid of 1, 000 workers.
The newcomers will hurt the three incumbent domestic airlines, and especially All Nippon Airways, which has the largest share of the domestic market.
On Wednesday All Nippon Airways canceled a domestic flight in Japan because of an error message on the braking system of a 787.
Nine days later, an All Nippon Airways 787 had to make an emergency landing in Japan after a battery started to give off smoke.
BBC: Dreamliner: Boeing 'may never find battery fault cause'
In the latest incident, Japan's All Nippon Airways cancelled a domestic 787 flight from Yamaguchi to Tokyo on Wednesday because of a brake problem.
Japan's leading airline, All Nippon Airways (ANA), has been using such e-wallets to compete with the country's formidably fast trains for more than five years.
Thirty-five percent of the major structural components are sourced in Japan, and All Nippon Airways was responsible for many ideas incorporated into the plane.
And beyond South-East Asia the airline has just broken into the Japanese market, teaming up with All Nippon Airways to launch a new domestic carrier.
ECONOMIST: One of Asia��s most successful carriers keeps on expanding
In a separate incident on 16 January on board an All Nippon Airways (ANA) flight, smoke was reported coming from the plane's battery but no flames.
Japan's All Nippon Airways (ANA) has said it will cancel all Boeing 787 flights until at least the end of May, in the latest blow to Boeing.
BBC: Dreamliner: Japan's ANA cancels more Boeing 787 flights
Boeing has backed the battery used in the Dreamliner after Japan Airlines and All Nippon Airways said they changed a number of them in the past few months.
All Nippon Airways said the Dreamliner grounding has had little impact on its earnings and profit shouldn't be significantly affected even if the suspension continues through next month.
The Japanese transport ministry said All Nippon Airways and Japan Airlines, the world's two largest Dreamliner operators, have already begun installing modified lithium ion batteries on their 787 jets.
The FAA and other authorities grounded the entire fleet after a second incident nine days later led to an emergency landing by an All Nippon Airways 787 in Japan.
Japan's two biggest airlines, Japan Airlines Systems Corp and All Nippon Airways Co Ltd, have expressed interest in a shorter-range model and are considered strong candidates for launch orders.
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