It is definately some sort of fungus, not a good sign. Looks like the bark has been damaged, that sort of fungus is the result of bark damage, not the cause. It does look as if there's quite a bit of damage to the trunk here and there - bark missing. Have you got a wider view of the whole tree?

If you want a healthy, happy, container-grown Japanese maple, you’ll need to plant your tree in a container that is about twice the size of the tree’s root system. It is imperative that the pot has one or more drainage holes. Keep the soil moist but not wet. Use good quality potting soil to fill the pot. Once the tree is potted, water it well. This helps to settle the roots in the soil. Don’t fertilize until spring, and even then dilute a water-based fertilizer to half-strength. If over time, you see that the roots of the Japanese maple in a pot touch the side or bottom of the container, it’s time for root pruning. Clip out the big, wood roots. This lets smaller roots develop.

Here are a few tips if you are considering dipping your toe into the sea of Japanese maples:

• Do your homework on cultivars to acquire the desired plant characteristics. Not all cultivars are readily available; however several specialty nurseries are listed on the Internet.
• Buy the shape and size desired. Forget coercing them.
• Location, location, location. Think long and hard when selecting the planting site.
• Well drained, slightly acidic soils with consistent moisture are fundamental needs for most.
• Plant on a slight mound in poorly drained soil or look for a new site.
• Afternoon shade or dappled shade is best for most. Too much shade may translate into slow growth, red-leaved types turn greener, variegated types may be predominately greener and yellows may not show gold undertones in heavy shade. In too much sun cutleaf and variegated forms can literally fry.
• Protect from wind such as on the east side of the house.
• Protect from late spring frosts. Japanese maples tend to leaf out early and a year of growth or entire plant can be lost. The goal is to encourage them to leaf out later which can be encouraged through mulching 3-4 inches with organic mulch such as wood chips and siting in a shady area that is slow to warm in spring. Be sure not to place mulch next to the tree trunk.
• First few years of special care will get your tree off to a good start. Keep soil moist but not soggy and mulch. Fertilize only if soil test reveals a need to lower the pH.