The Warriors have said they will appeal against the points deduction as the breach "did not affect the competitive balance of the competition".
The reigning champions will begin their campaign on -2 points.
In the seasons curtain raiser against St Helens this Thursday.
"Throughout this process, Wigan have been fully cooperative and transparent with no suggestion of concealment or deception and acceptance formally of the breach," said Warriors chairman Ian Lenagan.
"This is not an integrity or dishonesty issue, purely an administrative error by a new financial team in an exceptionally busy and disruptive circumstance.
"This breach clearly did not affect the competitive balance of the competition in 2017, yet the immediate deduction of two points does affect the competitive balance of the competition in 2019.
"In my experience of working in sport and sports governance, a points deduction is the last resort as a sanction for a significant level of breach. I am surprised that Wigan have been handed down a points deduction sanction for such a marginal offence."
The club have admitted at a tribunal, that the monies not included were from flight allowance payments to agents. And acknowledged that it should have been included in their 2017 valuation.
Lenagan commented the fine was "justified" and that he took "full responsibility" for the breach of cap salary.
In a Warriors club statement the club suggested they "gained no competitive advantage" and that 2017 was their "worst performance since 2006".