A federal education official said the department was looking into Lautenberg's request.
Various realignments of New Jersey's colleges and universities have been proposed over the last decade, but the merger of Rutgers-Camden into Rowan has prompted protests from faculty, students, and alumni at the Camden campus, and to some degree, within the larger Rutgers system.
Christie has remained adamant that the proposal, drawn up by a governor's task force led by biotech executive Sol J. Barer, go forward by July 1.
Lautenberg's public correspondence Monday specifically questioned whether the merger is being proposed to benefit Cooper University Hospital, of which George Norcross is chairman. Cooper and Rowan have partnered to open a medical school in the fall.
The governor's office dismissed Lautenberg's allegations.
"The intention of the merger plan is to create medical and research centers of excellence," Christie spokesman Michael Drewniak wrote in an e-mail. "Sen. Lautenberg has apparently chosen not to be a positive participant . . . and instead is engaging in over-the-top correspondence like this, full of unsupported innuendo and political vindictiveness."
Lautenberg, 88, who is serving his fifth Senate term, has been at odds with George Norcross and Christie for years.
In 2010, Christie told New York magazine, "I don't really care what Frank Lautenberg has to say about much of anything," after the senator criticized his decision to kill a $8.7 billion railroad tunnel project connecting North Jersey and New York City.
And in 2008, Lautenberg was enraged when George Norcross supported U.S. Rep. Robert Andrews (D., Camden) in an unsuccessful campaign to unseat the senator.
Lautenberg sent a letter to Christie last month questioning the merger; his office said he was still waiting for a response.
Now he is asking Duncan to investigate the merger on the grounds that Rutgers-Camden students receiving federal assistance could face higher costs at Rowan.
Annual tuition and fees at the two schools are within $750 of each other, but according to Lautenberg's office, students at Rowan pay on average $5,000 to $8,000 more when factoring in financial aid - based on federal education data.
This "may lead to increased rates of student borrowing" and for who those who cannot "afford the higher price tag," the possible need to "reconsider their education choices," Lautenberg wrote.
Rowan spokesman Joe Cardona said that calculation was based on old data.
"We're putting $2 million more into financial aid now than we did two years ago," he said. "We've worked to keep our tuition down."
Lautenberg also addressed a theory that has been gaining momentum among Rutgers faculty that the merger was a means to help Cooper University Hospital, whose credit rating is one level above junk status.
There is no indication were the merger to go through that Cooper, the region's largest hospital as measured by revenue, would become part of the new institution. But Lautenberg suggests that just being affiliated with a larger research university would mean more revenue through medical-school tuition and research dollars.
Norcross did not respond directly to an e-mail for comment. But Cooper chief executive officer John Sheridan Jr. dismissed Lautenberg's letter as "outrageous."
"The reasons for the proposed merger of Rutgers-Camden and Rowan have nothing to do with the funding of the medical school but have everything to do with correcting an imbalance that exists in higher education in South Jersey," he wrote.
Lautenberg's accusatory tone won him many fans among Rutgers-Camden faculty.
The letter was on up on Facebook by late afternoon and quickly circulated through campus offices and dormitories.
John Oberdiek, a law professor, said the political mechanisms at work behind the scenes were a frequent topic of conversation among fellow professors.
"I'm not going to speculate, but it's worth looking into," he said.
Contact James Osborne at 856-779-3876 or email@example.com, or follow on Twitter at @osborneja.