The commission said it was "profoundly disturbed" by "repeated systemic failures and pervasive culture of non-disclosure" at the company.
The decision follows the commission's investigative report earlier in April that concluded that former executives of Wynn Resorts concealed sexual misconduct allegations against billionaire founder Wynn.
Brian Kelly, Wynn's lawyer, had said at the time that his client "denies all allegations of non-consensual sex and nothing in this report changes that."
The Massachusetts Gaming Commission released its decision after a year-long investigation and three-day hearing into allegations of sexual assault, misconduct and other inappropriate behavior and how Wynn Resorts handled them.
However, the commission added that there was not enough evidence to revoke Wynn Resort's gaming license.
The Las Vegas-based company received its Massachusetts license in 2013, allowing it to move forward with building the 671-room "Encore Boston Harbor" in Everett, Massachusetts. It is expected to open in June.
The watchdog said it would impose a $35 million fine on Wynn Resorts and a $500,000 fine on Chief Executive Officer Matthew Maddox, in addition to license conditions including an independent monitor to oversee the company's adherence to policies and organizational changes.
"We are in the process of reviewing that decision and considering the full range of our next steps," Wynn Resorts said in an emailed statement.
The report by the commission's investigations and enforcement bureau followed a January 2018 article by The Wall Street Journal detailing allegations that Wynn had engaged in a decades-long pattern of sexual misconduct.
His subsequent exit as the company's chief executive and sale of his stake in Wynn Resorts made him one of the most prominent executives to lose his job amid the #MeToo movement, which has highlighted longstanding patterns of sexual harassment and abuse in major U.S. institutions.
The commission said in its decision that Wynn Resort's culture favored the CEO in ways that left the "most vulnerable at great risk."
"While the company has made great strides in altering that system, this commission remains concerned by the past failures and deficiencies," the 54-page decision said.
Nevada casino regulators, following a similar investigation, in February fined the company $20 million.
(Reporting by Ismail Shakil in Bengaluru and Nate Raymond; Editing by Cynthia Osterman)