Getting the urine out has been a problem for earlier prototypes, causing them to balloon under the pressure.
The Japanese team got round this by growing extra plumbing for the kidney to stop the backlog, PNAS reports.
Although still years off human trials, the work helps guide the way towards making organs for people, say experts.
In the UK, more than 6,000 people are waiting for a kidney - but because of a shortage of donors, fewer than 3,000 transplants are carried out each year.
More than 350 people die a year, almost one a day, waiting for a transplant.
Growing new kidneys using human stem cells could solve this problem.
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