The U.S. attorney's office accused Modern Continental of knowingly using the wrong epoxy to hold up concrete anchors that failed in the 2006 ceiling collapse in the Interstate 90 Connector Tunnel.
It also accused the company of knowing about poor workmanship on slurry walls in the I-93 Tip O'Neill Tunnel before portions of the walls blew out in 2004.
Modern Continental was charged in federal court with making false statements, submitting false time and materials slips on contracts and wire fraud. If convicted, the company faces up to $24.5 million in fines, as well as restitution payments.
"This is yet another example of the ongoing commitment by the Big Dig Task Force to vigorously investigate those who have perpetrated a fraud on American taxpayers," said U.S. Attorney Michael Sullivan.
In a statement, Modern Continental called the charges "completely unfounded and without merit."
The company said the charges were "an attempt after the fact to criminalize actions" that were approved by state officials.
The ceiling collapse in July 2006 killed 39-year-old Milena Del Valle, who was crushed when tons concrete dropped on a car driven by her husband.
The U.S. attorney's office alleges that the company knew in December 1999 that the epoxy used to secure the ceiling's concrete anchors wasn't appropriate for long-term loads, but continued to use it anyway and then certified that work was properly done.
The company also allegedly certified that defective concrete panels in slurry walls in O'Neill tunnel were built to specifications, when it knew they weren't. A slurry wall blew out in September 2004, causing water to pour into the tunnel and a major traffic problem.
Federal prosecutors also say Modern Continental systematically overbilled the Big Dig in a scheme that totaled hundreds of thousands of dollars.
In its statement, the Cambridge-based company said its overbilling was a result of bookkeeping errors that were fixed. It said the company underbilled the project for other time and work, and ultimately charged less than it was owed.
Modern Continental said project officials knew certain slurry wall panels were built with slurry that didn't meet specifications, and in some cases specifically approved it. The company said there was no evidence that affected the quality of the finished panels.
The company also pointed to the National Transportation Safety Board's investigation into the 2006 ceiling collapse, which found that Modern Continental didn't know the epoxy being used to secure the concrete anchors was unsuitable for that use.