We have not been able to use our jacuzzi tub in our upstairs bathroom because every time we try to fill it with hot water after a few minutes it starts coming out rusty. We had the hot water heater replaced last year and have had the company come back to check the tank to make sure that isn't where its coming from. The tank is brand new and was drained 3 times already. That is not where the problem is coming from. What could be the problem? The water authority came also and said that it could not be their problem because it only happens with the hot water.

What type of pipes do you have? Copper, plastic or galvanized?

The tank is brand new and was drained 3 times already. Do you see any rust when you drain the tank? BTW. You don't have to drain the tank, you flush it. Let me show you how.
For long life and fewer troubles you should keep your heater clear of mineral build-up by FLUSHING NOT DRAINING on a regular schedule. Attach a hose to the boiler drain at the bottom of the tank. With the pressure on, open the boiler drain and let it run until the water runs clear. You will see a spurt of red,(rust) followed by white or yellow grains,(lime or calcium carbonate). This shouldn't take more then a few minutes. Do this monthly to keep it clear. Now flush out your hot water lines on ALL fixtures that are affected . Now pull each aerator and clean the screens. Be sure you put them back together the same way you took them out. Don't forget to flush it out every month. Your heater will thank you for it. Hope this helps and thank you for rating my answer, Tom

You may have a section of old pipe somewhere in the wall that discolors water...

This is a brand new tub and all brand new piping leading to it. We replaced all the piping and used new when we installed this tub about 2 yrs ago and it is only in this jacuzzi tub no other faucets

And you took this "brand new piping" off from a main made of -plastic, copper or galvanized? Tom

and you took this "brand new piping" off from a main made of -plastic, copper or galvanized? Tom

All the pipes were copper.

after a few minutes it starts coming out rusty. If it took running the hoit water for a "few minutes" this would indicate that the problem's back down the line near the heater. You wouldn't have galvanized nipples or heat trap nipples, (see image) that come out of the hot and cold inlets on the heater would you? Regards, tom