Here it says we blew up their hydrogen production which put a stop to it.
The Japanese government withdrew funding for the program around the same time that Allied forces blew up Japanese hydrogen plants, making the commodity needed to fill the balloons scarcer than ever. Plus it was unclear whether the weapons were working; security was so good on the U.S. side that news of the balloon bombs’ arrival never got back to Japan.
Forensic geology played a part in determining where the balloon bombs were being launched.
“When the balloons made landfall, there were no obvious clues as to where they originated. But forensic geology, then in its infancy, was able to pinpoint Japan as the point of launch. When Col. Sigmund Poole, head of the U.S. Geological Survey military geology unit at the time, was given sand from one of the balloon’s ballast bags, he is alleged to have asked, “Where’d the damn sand come from?”
His team of geologists knew it wasn’t a type of sand found in North America or Hawaii. “Japan was a logical guess,” said Tewksbury. The sand was unique enough to narrow the source down to two areas on the island of Honshu. “Most likely it had been coming from a small chunk of beach east of Tokyo,” he added.”
I recall a 1996 New Yorker Magazine article which goes into more detail about the forensic geology used in determining the exact location. It’s here behind a pay wall: http://www.newyorker.com/magazine/1996/01/29/the-gravel-page-the-gravel-pageballoons-of-wardeath-of-an-agent