More than 8,500 employees in those states will receive lump sum payments of $750.
Company spokeswoman Jackie Barry blames the problem on a computerized payroll system that went online as scheduled just days into the chaotic recovery from the late October storm.
New York Attorney General Eric Schneiderman says he reached a $4.8 million settlement with National Grid. Massachusetts Attorney General Martha Coakley earlier announced a $270,000 fine against the utility for violations of wage and hour laws.
The company has agreed not to pass the costs on to ratepayers.