Because the memory controller is in the processor, ECC support depends on the processor, not the chipset or motherboard. You'll need a Xeon processor to use ECC memory on X99.
The memory controller determines the types of memory that can be used. Because most systems today have the memory controller on the processor (where it is called an integrated memory controller, or IMC), the type of memory you can use depends on the processor, not the chipset or motherboard. Most consumer processors, except for certain desktop Pentium and Celeron parts, cannot take advantage of ECC memory. Xeon processors, which are designed for server/workstation use, do support ECC.
The Intel X99 chipset, with its LGA2011-3 socket, can accept either consumer (Haswell-E) Core i7 processors or server/workstation (Haswell-EP) Xeon E5 v3 processors. If your application requires ECC memory, you'll need to invest in a Xeon processor. A system equipped with a Core i7 processor and ECC memory will not be able to use the ECC functionality of the memory and may not boot at all.
However, registered (buffered) memory, which is used in some servers, is mechanically and electrically incompatible with unregistered (unbuffered), memory. Although X99 by itself does not prevent the use of registered memory (again, that depends on the processor's IMC), most X99 boards (except for some workstation boards such as the Asus X99-E WS) do not accept registered memory modules. ECC modules may or may not also be registered, so be sure to check the product specs before buying.