It was bad. It was so bad there's a Japanese saying, 陸海軍あい争い、余力を以って米英と戦う, meaning that [the war] was a fight between the army and the navy, who then fought the US and British with their remaining strength.
The army and the navy competed for resources, had competing objectives, and set up parallel logistics so they wouldn't need the other. So the army made their own Submarine model, the Maru Yu, to try and smuggle supplies to their forces in the solomon islands, and even refurbished a passenger liner into something vaguely like an escort aircraft carrier, the Akitsu Maru, with the intention of using it to support amphibious assaults. Over on the navy side, they had their own infantry and paratroop forces. They both developed aircraft without much cooperation (though that wasn't necessarily limited to the Japanese). Their command structures were pretty much entirely parallel and not unified under a single commander in chief like the US.
The whole atmosphere at the time in Japan very much promoted rivalries and competition, both in politics and the military. Incidents of individuals taking it upon themselves to eliminate political or factional rivals were so common that it's been called "Government by Assassination".
Possibly the biggest problem was their having incompatible parallel objectives. Before the war, when securing natural resources was a problem, they had to choose between the northern strategy of attacking Russia to claim eastern Siberia, or the southern strategy of seizing the east indies from the Dutch, putting them in conflict with the British and Americans. The northern strategy was favored by the army, the southern by the navy, who were unable to contribute to the war in China very much and wanted their own chance for glory. This led to all their prewar planning being split. The army did most of their planning for a theoretical war with the Soviets, the navy did most of their planning for a war with the Americans and British.
The decision to pursue the southern strategy was a major factor in what lead to Pearl Harbor, pulling the US into the war. Who knows what could have happened if they'd made the decision to pursue the northern strategy instead. Instead of having a nonaggression pact with the Soviets, they could have opened up a second front when Barbarossa happened, allowing Germany to have greater success in their march east. It also would have delayed the US's entry into the war, giving Hitler even more time to deal with Russia and consolidate power.
Throughout the rest of the war you had the problem that the Army was overextended in China and couldn't provide the support the Navy wanted to pursue their plans. Following their initial push after Pearl Harbor, the Navy was making all sorts of fanciful plans to invade Hawaii or Alaska and Panama and so on, but they were hampered by the fact that the army was tied down in China and didn't have enough troops to support them.
If you want to know more, I might recommend Shattered Sword. It's specifically about the battle of midway from the perspective of the Japanese rather than about the inter-service rivalry, but it's extremely well written and goes into more detail about the competing objectives and lack of cooperation between the service branches.