Despite the fine, the Commission has allowed the operator to keep its state casino license and continue with plans to open its $2.6bn Encore Boston Harbor resort in June.
The MGC has also fined Wynn Resorts’ current CEO Matthew Maddox $500,000 for his "clear failure" to investigate at least one complaint. The MGC now requires the company to be reviewed by an independent organisation.
A statement from the regulator said: "While the company has made great strides in altering that system, this Commission remains concerned by the past failures and deficiencies.
"Given our findings, it is now in the interest of the Commonwealth that the gaming licensee move forward in establishing and maintaining a successful gaming establishment in Massachusetts."
Following a similar investigation, Wynn Resorts was fined by Nevada regulators to the amount of $20m, but was also permitted to keep its casino license.
Both Nevada and Massachusetts regulators had focused on how long the company officials were aware of the allegations against Wynn and how they responded, rather than the validity of the claims.
Wynn has denied allegations of misconduct, claiming the relationships had been consensual, but resigned as CEO when they were first reported.
