Russia's prosecutor general told Putin more than 9,000 mobilized troops were called up illegally.
In a face-to-face meeting, he said their health was why many shouldn't have been sent to fight in Ukraine.
Reports last year said Russia had called up students, elderly people, and those with health issues.
In a sitdown meeting with Russia's president, the country's prosecutor general said that thousands of troops who were mobilized to fight in Ukraine last year were conscripted illegally.
Igor Krasnov told Russian President Vladimir Putin that almost 9,000 reservists were mobilized illegally, according to a transcript of their conversation released by the Kremlin on Tuesday. He said that many of them should not have been sent in the first place because of ill health, and were later returned to Russia.
Krasnov also said there had been issues with paying the troops.
In his conversation with Putin, Krasnov said that the mobilization "revealed a lot of significant problems."
In September, Russia announced a partial mobilization of 300,000 troops, which it said was completed in October. This came after major battlefield setbacks for Russian forces, which had expected a quick victory following the February 2022 invasion of Ukraine.
Putin said in December that 150,000 of those troops had been sent to serve in Ukraine, with the rest still in training in Russia.
The military call up resulted in tens, if not hundreds of thousands of young Russians leaving the country by plane and over its land borders in the weeks that proceeded it.
Putin admitted last September that Russia had made "mistakes" in its mobilization, after reports that students, people without combat experience, the elderly, and those with health issues were among those who had been called up to fight, when only reservists were supposed to have been drafted.
Krasnov told Putin that Russia had been forced to "reconsider approaches to the organization of military registration," and had created databases of available military personnel.
Widespread issues related to Russia's mass mobilization have long been reported, including a lack of training and equipment. Some soldiers were drafted, trained, sent to Ukraine, killed, and returned home in body bags within a month of the announcement - a rapid timeline that would be unheard of in a Western army.
Experts and defectors also say that Russian generals used the troops like cannon fodder.
In the transcript of the conversation released by the Kremlin, Putin praised Krasnov's work, and asked him to keep monitoring the "rights" of mobilized Russians.
This comes as Russia is expected to announce another round of mobilizations, though the numbers are unclear.
Ukraine and its allies say they expect a fresh Russian offensive in the spring, with Ukrainian intelligence warning earlier this month that Russia plans to mobilize 500,000 additional troops.
NATO Secretary-General Jens Stoltenberg said on Monday that Russia is preparing to mobilize more than 200,000 troops, while the UK ministry of defense said in December that Putin had been presented with plans to expand Russia's military by around 30%, to 1.5 million active personnel.
The release of the transcript between Putin and Krasnov is likely an effort by the Kremlin to reduce concerns in Russia that any future mobilizations will be as ill-prepared as the last one.