Parshall and Tully had a pretty good discussion of this in Shattered Sword, their work on the Battle of Midway. Essentially, yes, their damage control was sub-par, for a whole host of reasons; some of them were inherent to Japan's situation and some of them were IJN management failures.

First, the issues with Japan as a whole. One of the disadvantages that Japan had was that their countryside had a lot less in mechanical tools, especially in agriculture. The average Japanese recruit was unlikely to have much experience with tinkering, fixing, or maintaining modern equipment. Because of this, officers needed to take a much more active role in technical tasks, and enlisted who had those skills were valuable in roles where they were essential - the engine room, aircraft maintenance, etc. What was left was even less technical than average, which was a big drawback for damage control.

Japan also lacked the US's industrial resources, and its warships were not fitted with the same complement of equipment. US sailors had much wider access to things like hand pumps to assist in firefighting. (They also used a lot more in the way of wood for internal ship fittings, so things were that much more flammable.)

Japanese ship design itself was heavily oriented toward speed and offensive firepower; inevitably this came at the cost of armor and internal structure. (Not, strictly speaking, a damage control problem - but it meant that Japanese ships were less resilient in the first place.) This was inevitable given Japan's military doctrine and the necessity of facing a numerically superior US fleet, and also dovetailed with Japanese military philosophy, which heavily supported the attack over defense and indeed survival.

Three institutional problems exacerbated the general issues Japan had to deal with. The first is that there was a failure to look at damage control in a systemic fashion. US ships had thorough documentation of their (really quite complex) systems of valves, doors, bulkheads, etc., and various plans by which damage control parties could quickly isolate entire areas of the ship, complete with checklists that enabled this to be done both quickly and thoroughly. Japan didn't have anything similar to this, so damage control officers had to rely on their own familiarity with the vessel's layout and their own memory of what needed to be done. At least one vessel that we know of was lost almost entirely through a damage control error of this type (Taihou, which had damage from a torpedo mostly contained until fuel fumes were vented throughout the ship, precipitating a fuel-air explosion and the loss of the carrier.)

This was complicated by the fact that damage control was a specialized task within the IJN; it was considered the province of particular officers. (The US, by contrast, drilled -everyone- in damage control, considering it as essential to the sailor as marksmanship is to a soldier.) This meant that the direction of damage control efforts, and the key information necessary to make them useful, was in the heads of a few individuals - and if those individuals were wounded or killed by whatever did the damage to the vessel, that could cripple its efforts at damage control.

There's one more element that Parshall and Tully only touch on - Japanese military discipline was savage. Officers and NCOs routinely beat those in their command for even minor infractions; this was no recipe for encouraging initiative among the lower ranks. (For some illustrative examples, you can refer to Hata's Japanese Destroyer Captain - he was a Japanese officer opposed to the practice and encountered it in many places, even at Etajima, Japan's naval academy, where some of his classmates were beaten so thoroughly by their upperclassmen that they were maimed and rendered unfit for service. And these were their elites, picked officer candidates!)

You couldn't really say how much of it was just "Japan being 1940s Japan" and how much of it was "institutional failures within the IJN" - the latter were, of course, pretty heavily influenced by the former.