A packed 28 kg domestic parcel is above ordinary Yu-Pack’s 25 kg limit. Weight Yu-Pack, called 重量ゆうパック, is an option for eligible parcels over 25 kg and up to 30 kg, within a three-side total of 170 cm. Whether to keep one box or split it requires a comparison of the actual fares and handling conditions—not just the weight. Japan Post: ordinary Yu-Pack, Weight Yu-Pack
This is desk research, not a test shipment. The examples below are hypothetical, and assume the contents are otherwise acceptable.

Compare a surcharge with a second parcel, not with zero
Japan Post lists Weight Yu-Pack at the applicable ordinary base fare plus ¥620. The base fare depends on the size and route. Splitting the contents removes the need for the heavier service only if each finished parcel meets ordinary-service conditions; it also creates a second fare. Japan Post: Weight Yu-Pack fares
Use three actual quotes: W for one Weight Yu-Pack, A for the first ordinary parcel and B for the second. Each quote should include the discounts actually applicable to that option. Then compare:
Extra cost of splitting = A + B − W, before additional packing materials.
For example, suppose the final quotes were W = ¥2,300, A = ¥1,200 and B = ¥1,300. These invented figures illustrate the arithmetic; they are not Japan Post rates for any route. Splitting would cost ¥200 more before materials: 1,200 + 1,300 − 2,300 = 200.
If the two smaller-parcel quotes instead totalled ¥2,100, splitting would save ¥200 before materials. The conclusion changes with the actual size bands, route and discounts. There is no rule that two lighter parcels are always cheaper, or that the ¥620 surcharge is always the cheaper choice.

Reweigh after repacking
Do not divide 28 kg by two and assume the result is the weight of each new parcel. That calculation divides the original packed parcel, including its old box. Two new boxes and their protection create a different total.
For a separate hypothetical example, suppose the contents weigh 27 kg and the original packaging weighs 1 kg. If you divide the contents evenly and each new package adds 0.8 kg, each finished parcel weighs 13.5 + 0.8 = 14.3 kg. Together they weigh 28.6 kg, not 28 kg. Their dimensions also need new measurements.
Compare finished parcels that protect the contents appropriately. Removing necessary packaging to fit a price category is not a valid cost comparison. If an item cannot reasonably be separated, the two-box option may not exist at all.
Check whether the heavier service fits the delivery task
Japan Post’s Weight Yu-Pack page specifies post-office counter acceptance, excludes convenience-store handling, and says delivery generally takes about one additional day compared with ordinary Yu-Pack; some destinations take longer. Chilled and security services are unavailable. These conditions can rule out the option before price becomes decisive. Japan Post: locations, delivery and available options
For example, a deadline-sensitive sender should compare delivery estimates for both options rather than add one day to a guessed ordinary delivery date. A sender needing a service excluded from Weight Yu-Pack must resolve that requirement rather than select it solely because 28 kg fits.
Splitting also creates two items for the recipient to identify and check. Record which contents go into each package, and retain the dispatch records for both. This is an editorial planning suggestion, not a guarantee that separately mailed boxes arrive together.
Do not create one parcel by tying two boxes together
Japan Post specifically excludes bundled packages held together with string or tape from Weight Yu-Pack. It also describes a limited exception for lightweight outer packaging taking clearly identified contents of no more than 30 kg above that gross weight. Treat that as a counter-confirmation case, not a general allowance above 30 kg. Japan Post: size and weight conditions
Before deciding, write down the packed dimensions, weight, route, required services, delivery estimate and final quote for each viable arrangement. Keep the contents identical in both comparisons. That makes the choice reviewable and prevents a small apparent postage saving from hiding extra packing costs or an unsuitable service.