According to the article it seems they were taking a very long view on this (unless there is some error):
"The diary of Masa Takeuchi, a worker assigned to Nishina's thermal diffusion separation project, says Nishina wanted to process hundreds of tons of uranium at the rate of 300 mg per day, according to the U.S. journal Science."
Basic math: 300 mg per day is about 0.1kg per year, so processing hundreds of tons would take millions of year.