Marvel Entertainment Inc. has filed suit in New York County Court against MGA Entertainment Inc., claiming that the Van Nuys toymaker breached the terms of its licensing agreements with the comic book entertainment company.

It’s another problem to emerge for MGA, which lost a court battle over ownership of its Bratz dolls to Mattel. Punitive measures in that case are pending.

New York-based Marvel claims in its Jan. 2 lawsuit MGA owes the company $1.88 million for failing to pay licensing fees, and for violating the terms of several licensing agreements by making toys related to Spider-Man and Ghost Rider, which were excluded from the deal.

MGA denies the allegations.

In the suit, Marvel claims a November audit report revealed that MGA owes the company at least $1.1 million from unpaid licensing fees, including a $375,000 minimum guarantee payment that was due by Jan. 1.

According to court documents, Marvel is additionally seeking at least $780,000 from MGA based on the sale of the products that were excluded from its licensing agreement.

“MGA has reviewed the complaints filed by Marvel Entertainment and Spiderman Merchandising and has concluded that the claims alleged are without merit in either fact or law,” MGA Chief Executive Isaac Larian said in a statement provided to the Business Journal. “MGA intends to vigorously defend itself and is confident that it will ultimately prevail at trial.”

MGA has already been bruised in a court battle in with Barbie maker Mattel Inc. over the popular Bratz fashion dolls.

A federal judge is deciding whether to allow MGA to sell and manufacture the Bratz doll line through the end of the 2009 retail season. In December, El Segundo-based Mattel won a permanent injunction banning MGA from making and selling Bratz dolls, which were found to infringe on Mattel’s copyrights.

MGA is appealing the federal judge’s order that bans MGA from making and selling Bratz.