The WPB placed penicillin under a wartime allocation system on 16 July 1943. All supplies were designated for use by the armed forces and the Public Health Service. Penicillin production in the United States ramped up from 800 million Oxford units in the first half of 1943 to 20 billion units in the second half. The US government built six production plants at a cost of $7.6 million (equivalent to $ million in ). These were sold after the war to the companies that operated them for $3.4 million (equivalent to $ million in ). Another sixteen plants were built by the private sector for $22.6 million (equivalent to $ million in ), although $14.5 million (equivalent to $ million in ) was approved for accelerated depreciation under which the cost could be written off in five years instead of the usual twelve to fifteen.
US penicillin production rose from 21.192 billion units in 1943, to 1,663 billion units in 1944, and an estimated 6,852 billion units in 1945. By June 1944, Pfizer alone was producing 70 billion units per month. Monthly production dropped off after July 1945 due to a shortage of corn-steep liquor. The price offered by the CMR for a million units fell from $200 in 1943 (), which was below its manufacturing cost, to $6 in 1945 (). 
The chairman of the NRC committee on chemotherapy, Chester Keefer was responsible for administering the equitable distribution of penicillin for civilian use on behalf of the CMR. As the news of the effectiveness of penicillin spread, he had to deal with a large volume of requests for the drug. Supplies for civilian use were initially small, and penicillin was initially provided only for cases with a high mortality rate that did not respond to other forms of treatment.  In January 1943, he reported to OSRD on the results of the treatment of the first 100 patients; by August, 500 patients had been treated. Military requirements consumed 85 per cent of production in 1944. This dropped to 30 per cent in 1945, but civilian demands for penicillin exceeded allocations. 
By April 1944 supply and demand had exceeded the ability of one man to administer, and the task was handed over to a Penicillin Producers Industry Advisory Committee that distributed supplies through a network of depot hospitals. By 1945, there were 2,700 depot hospitals holding supplies of penicillin, and another 5,000 hospitals receiving supplies through them. Penicillin became commercially available by the end of the year, by which time the United States was exporting 200 billion units a month. By 1956, only twelve of the twenty-one firms that produced penicillin during the war were still involved in its manufacture.