Be flexible in your start and end location
Direct flights to Japan can be expensive - this guide teaches you the best way to bypass these big airports and get cheaper access to other parts of Japan
If you are flying from Singapore to Japan, chances are you will be subjected to skyhigh flight ticket prices especially during peak period.
Tip 1 - Check neighbouring airports or reverse your routes
Tokyo - no good neighbouring airports, best bet is reverse your routes
Osaka can consider Kobe, Nagoya
Fukuoka/Kyushu can consider Hiroshima, Kagoshima, Nagasaki if you are travelling Kyushu
Tip 2 - Make use of ferries
Busan has a daily overnight cruise to Busan, and flights into/out of Busan are generally cheaper. When adding in an overnight trip to Busan, overall can be cheaper.
Busan > Fukuoka (ideal)
Busan > Osaka (only if it is a trip on its own)
One thing great about JAL and ANA is that they provide free connecting domestic flights, which means if you use them to fly into smaller airports via Tokyo or Osaka, the cost would be the same as a Singapore-Tokyo/Osaka return flight. So if you can fly closer to your start/end destinations that would save you quite a bit of money - shinkansen can actually be quite expensive.
Most people miss out on this though, because they book return flights into and out of Tokyo/Osaka, then book transport to other parts of Japan because of the flexibility. This can affect your trip flexibility and incur you more transport cost. The biggest culprits are on these routes:
Hokkaido - flying in and out of Sapporo Airport (CTS) instead of flying into Asahikawa Airport and out of Hakodate Airport
Chugoku/Shikoku (e.g. Hiroshima, Tottori, Okayama, Kagawa) - flying into Osaka instead of Hiroshima Airport (HIJ), Tottori Airport (TTJ) and Kagawa (Takamatsu Airport)
Kyushu - flying into and out of Fukuoka instead of taking one-way into Fukuoka, and one-way out of Kagoshima or Kumamoto Airport
If your trip is more linear (e.g. travelling from the north of Kyushu to south of Kyushu), be open to flying into domestic airports. You may also be able to spend a few days in Tokyo as a layover for free! With low cost carriers joining the competition, it is not always cheaper to use the free connecting domestic flight. Just remember to check - you might save some money!
Hokkaido is a popular destination because it can offer a cooling experience during summer, and a winter wonderland during Feb/Mar. However, there is only one major airport - New Chitose Airport at Sapporo, but most of the itineraries span from East to West (winter) or North to South (summer).
Instead of spending the extra money to travel from Sapporo to the west (Abashiri and Shiretoko for drift ice walking and exploring one of Japan's most untouched national parks) before uturning towards the east (Hakodate for seafood and beautiful night sights), it is way more straightforward to start from the west and head to the east - exactly what I am doing in Jan/Feb 2027.
To preface, I am not suggesting flying into domestic airports by transferring at one of the main gateways. Domestic flights are typically expensive and won't save you much. Instead, I would suggest that you fly directly into the smaller international airports.