In popular media , Japanese soldiers are shown to use their swords for close combat. Was this a common occurrence? Were soldiers of the era familiar in their use? Did the japanese army issue them or where they personal weapons?
Are there any battles of note which involve a Japanese soldier using his sword to great effect during the war?
The wearing of Japanese style swords by front line officers was only re-introduced to the Imperial Japanese Army in 1934 by Araki Sadao, the flamboyant leader of the Imperial Way faction. This faction was opposed more or less successfully by Army factions with a more realistic view of warfare and Japan became engaged in their major war China three years later in 1937. So there wasn't much time for sword usage to become institutionalized in the Army before the country went to war. Japanese officers may have had some Kendo experience but it wasn't in any way a focus of their overall training, which for many was quite hasty. Japanese Army doctrine did emphasize morale and spirit, but it also acknowledged the importance of firepower and combined arms. The sword was a bit of patriotic window dressing intended to boost morale.
Swords in close combat, or indeed close combat in general, wasn't common. Grenade and bayonet charges were a feature of Japanese doctrine, but the idea was that the enemy ran away before contact. Finding the enemy flanks and making flank attacks or attacking at night to increase the enemy's confusion and demoralization were a feature of IJA doctrine. In China, where the IJA did most of it's fighting, the Japanese army usually had superior firepower. Even in the Pacific theater, where allied units had a firepower advantage, Japanese units primarily fought with modern weapons in a modern way, except in isolated cases when things were extremely desperate.
The Japanese army did issue the officers swords. They were produced by order of the military in huge quantities. There are anecdotes of personal weapons or family heirlooms being used, but if the Japanese government hadn't needed to issue hundreds of thousands of swords they would not have produced them.
I am personally unaware of any notable instances of swords being effectively used in combat during the war. There are numerous accounts of swords being used to mistreat and execute prisoners, and one famous incident where an IJA Lt. Colonel assassinated a general in a factional dispute within the army.