Ma identified the industry's "996" work schedule, which refers to a twelve-hour workday over six days a week, as a "huge blessing" for young workers, sparking worldwide social media outrage.
"As I expected, my comments internally a few days ago about the 996 schedule caused a debate and non-stop criticism", Ma wrote.
Ma's earlier comments stoked a fierce ongoing debate over tales of programmers and founders dying from unrelenting stress.
Defending the 996 work time, the tech-giant founder referred to the fact that in the tech industry many people are unemployed or working in companies that are close to bankruptcy.
Ma added that companies that thought they could profit by forcing staff to work overtime were "foolish" and doomed to fail. Chinese tech workers protested against labour conditions on the online code-sharing community GitHub in March under the banner 996.ICU, which quickly became the site's most popular topic.
Users uploaded screenshots of conversations in which they were asked to work late in the evening.
"By following the "996" work schedule, you are risking yourself getting into the ICU [Intensive Care Unit]", according to a description posted on the "996.ICU" project page. Ma's comments come as the mental and physical repercussions of overwork are becoming more widely studied, discussed, and recognized.
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In the Weibo post on Sunday, Ma said: "Real 996 should be spending time learning, thinking and for self-improvement".
One user commented on the discussion forum Zhihu: "Most of today's companies are machines that can not stop running".
Beyond Ma, several of China's most prominent industry figures have also weighed in on the controversy.
"If you find a job you like, the 996 problem does not exist; if you're not passionate about it, every minute of going to work is a torment", Ma stressed.
Ma's comment followed his remarks on Thursday that working overtime could be a "huge blessing" for young workers who found careers they were dedicated to.
Mr Richard Liu, chief executive of Alibaba arch-foe JD.com, said in a recent post on his WeChat Moments that, while he would never force staff to work a 996 schedule, people who slacked off were not considered his "brothers". "If you do not work longer than others to make more effort, how can you achieve the success you want", he questioned Alibaba employees.