Beth Israel Medical Center has agreed to cough up more than $13 million to settle allegations that it fraudulently inflated its fees to boost payments from Medicare.

A civil suit filed by the feds accused the East Side hospital of “turbocharging” its rates between 1998 and 2003 for certain treatments “that either were not extraordinarily costly or were much less costly than Beth Israel made them appear to be.”

But because of a statute of limitations, the government could only seek damages and penalties covering patients who were discharged since February 2002.

Manhattan US Attorney Preet Bharara said yesterday that the deal “demonstrates our commitment to pursuing those whose conduct drives up the costs of health care.”

Hospital spokesman Jim Mandler said Beth Israel “was content that this long-ago issue has been settled.”