What went in did come out.
First, it was Shimane Prefecture where they found the manure made from cow dungs and urine with radioactive cesium in excess of the hastily decided provisional safety limit for manure and composts (400 becquerels/kg). The level of radioactive cesium ranged from 152 to 1083 becquerels/kg. The cows had eaten radioactive hay from Miyagi Prefecture. (From Asahi Shinbun 9/11/2011, original in Japanese).
Now it is Niigata Prefecture. Unlike Shimane Prefecture who just tested the manure at the JA (Japan's agricultural producer co-op) stations, Niigata also tested the manure made at individual farms (sampling), and even higher amount of radioactive cesium was detected.
According to the Niigata Prefecture announcement on August 13, of the individual farms, only Niigata City and Sado City (on the island of Sado off the coast of Niigata) tested below the detection limit. Even if the manure at the individual farms tested high, the numbers at the the manure manufacturing depots were low, as the radioactive manure was mixed with non-radioactive manure. No radioactive iodine was detected anywhere.
(PDF file of the announcement, page 2, showing the numbers)
In the table above, the individual farms No. 5, 6 and 7 (radioactive cesium 260 to 1,100 becquerels/kg) are located in the same city as the manure depots No. 3 and 4 (ND to 10 becquerels/kg). The individual farms No. 3 and 4 (3,760 and 1,280 becquerels/kg) are located in the same city as the manure depot No. 2 (330 becquerels/kg).
But since the numbers at the manure manufacturing depots are low enough, it will probably be sold to other farms to be used in their fields, thus spreading the low-level contamination all over Niigata. In the eyes of the government and producers, they are "safe" as long as the numbers are below the arbitrary safety limit number that the government picked after the fact. Testing by sampling one or two farms in a city will be enough for them.
Niigata Prefecture has told the 9 farms whose manure exceeded this safety number (400 becquerels/kg) not to move their manure [to the depots], meaning the other farms and the farms whose manure weren't tested will continue to send their manure to the depots or use it on their farms or give it to other farmers.