Volodymyr Zelensky confirmed more than 30 people face criminal charges, with all regional officials in charge of military conscription removed.
He said bribery at a time of war is "high treason".
It comes amid efforts to bolster the armed forces, as Ukraine's counter-offensive operation continues.
A statement from the president's office said corruption allegations "pose a threat to Ukraine's national security and undermine confidence in state institutions".
Replacement officials will be chosen from candidates who have battlefield experience and have been vetted by the intelligence service, it continued.
Officials taking cash and cryptocurrency bribes or helping people eligible to be called up to fight to leave Ukraine are among the charges, said Mr Zelensky, in a video posted on social media.
Ukraine's general mobilisation rules mean all men over the age of 18 capable of fighting are eligible to be conscripted, and most adult men under the age of 60 are prohibited from leaving the country.
"We are dismissing all regional military commissars," he said.
"This system should be run by people who know exactly what war is and why cynicism and bribery at a time of war is high treason."
He said the conscription system "is not working decently", adding: "The way they treat warriors, the way they treat their duties, it's just immoral."
The corruption came to light after an inspection of local army offices.
Mr Zelensky said 112 criminal proceedings against 33 suspects have been launched against regional officials, and that abuses had been found across the country.
Neither Ukraine or Russia reveal how many of their soldiers have been killed since the February 2022 invasion, but both have sought recruits widely as attritional fighting continues.
The anti-corruption drive is the latest to be launched by the Zelensky government.
In January 11 officials accused of corruption left their posts and the head of the country's Supreme Court was detained in May over bribery allegations.
Corruption in public services has been a long-running problem in Ukraine and tackling it is one of the tests the country would have to pass to join Western institutions like the European Union.
According to Transparency International's Corruption Perceptions Index, Ukraine ranks 116th out of 180 countries, but efforts in recent years have seen its position improve significantly.