BOSTON (Reuters) - Three well-known U.S. universities, MIT, New York University and Yale, have been accused of charging millions of dollars in excessive fees to participants in their retirement plans, according to federal civil lawsuits filed on Tuesday.

The complaints against the three universities accuse them of breaching their fiduciary duties by causing the plan participants to pay millions of dollars in unreasonable and excessive fees for record keeping, administrative and investment services.

In the Massachusetts Institute of Technology complaint, Fidelity Chief Executive Officer Abigail Johnson is singled out because she sits on the school's board of trustees. Johnson's family controls Fidelity, which had $1.2 trillion in fund assets under management at the end of June, according to Morningstar Inc.

Fidelity spokesman Steve Austin said the company is not a defendant in the suit and declined further comment. MIT also declined to comment.

The $3.5 billion MIT plan is accused of hiring Boston-based Fidelity as record keeper without competitive bidding and offering dozens of Fidelity mutual funds as investment options, according to a lawsuit filed in U.S. District Court in Boston. The mutual fund options included retail shares, which are more expensive than institutional shares.

"Retail share class mutual funds are designed for small individual investors and are identical in every respect to institutional share class funds, except for much higher fees," according to the complaint filed by St. Louis law firm Schlichter, Bogard & Denton, which filed the suits against all three universities.

New York University spokesman John Beckman said the school has not had time to fully review the lawsuit filed against the school in U.S. District Court in Manhattan.

"But it seems worth noting that, first, decisions about our retirement choices are influenced by feedback from our faculty and other employees," Beckman said.

Yale, which faces a lawsuit filed in U.S. District Court in Connecticut, said it has not been officially served with the complaint.

"We are cautious and careful in administering our plans and we will defend ourselves vigorously," Yale spokeswoman Karen Peart said.

(Reporting By Tim McLaughlin and Ross Kerber; Editing by David Gregorio, Alan Crosby and Chris Reese)