"Just setting up my twttr…again (account suspension was an internal mistake)," Dorsey tweeted late Tuesday.
For about 15 minutes those trying to access Dorsey's account received a message stating that the account was suspended.
Only the company can suspend Twitter accounts, though users can deactivate their own.
The company did not respond to an AFP inquiry.
The incident came as Twitter is struggling to increase its user base and seeking a path to profitability.
Co-founder Dorsey returned as chief executive last year, but has yet to ignite growth.
Just weeks after reporting job cuts and a disappointing fiscal quarter, Twitter announced earlier this month that chief operating officer Adam Bain was leaving the company.
Twitter was widely reported to be in talks to find a buyer but no deal has materialized.
The company recently said it would cut nine percent of its workforce and discontinue its looping video application Vine in the coming months.
