After meeting his top military commanders, Zelenskiy said the commission would be headed by General Oleksandr Pavliuk, who is first deputy defence minister.
The decision follows Ukrainian media reports of corruption allegations against the head of a draft office.
Zelenskiy said he had ordered the urgent dismissal of the head of a draft office whose family was reported by the Ukrainska Pravda media outlet to own property and cars worth millions of dollars in Spain.
"I gave an urgent order to create a commission... and together with law enforcement units and the National Agency for Corruption Prevention to check all the heads of military draft offices in all regions of Ukraine so that they do not disgrace our state and the memory of heroes who die at the front," Zelenskiy said on Telegram.
In his statement, he also said he discussed the situation on the front lines, weapons supplies and the pace of production of Ukrainian defence companies.
Earlier on Friday, Zelenskiy said Ukraine's top security body decided to bring officials to justice over the deaths of three people who were locked out of a bomb shelter during a Russian missile strike.
Zelenskiy said the National Security and Defence Council had met and discussed the security of the Ukrainian people, judicial reforms and Ukraine's accession to the European Union.
"A quarter of bomb shelters in Ukraine and a third in Kyiv are unfit for use," Zelenskiy said, citing an audit of air raid shelters that he ordered following the three deaths on June 1.
"The decision of the National Security Council is to bring the guilty to justice, and to get all protective structures in the proper condition."
He provided no other details of the decision or who might be punished, but posted a video of top government and military officials raising their hands in a vote at a round table.
Oleksiy Danylov, the council's secretary, said earlier this week that "staff decisions" could be made during the meeting.
The deaths of the three people, after they rushed to a Kyiv air raid shelter that failed to open, caused public outrage.
Zelenskiy criticised Kyiv city officials and prosecutors put the head of Kyiv's municipal department for security under house arrest following an audit of air raid shelters.
After the bomb shelter incident, Kyiv mayor Vitali Klitschko said he bore some responsibility but that others were to blame, especially appointees of the president.
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