Homeland Security Committee Chairman Joe Lieberman, an independent, and Susan Collins, the panel's top Republican, said the departments of Justice and Defense had until Monday to provide the information or face legal action.
"We do not lightly reach this decision," Lieberman told a news conference.
Collins said they had no choice. "We have been stymied," she said.
Lieberman and Collins have been trying for months to obtain specific information about the shooting spree at Fort Hood in November that ended with 13 soldiers killed and many wounded.
An Army psychiatrist, Major Nidal Malik Hasan, has been charged by the military with 13 counts of premeditated murder and 32 counts of attempted murder. The case drew heavy criticism after it became known Hasan had been in contact with an anti-American Muslim figure sympathetic to al Qaeda.
The senators said their committee wanted access to documents and witnesses regarding what the FBI and Defense Department knew about Hassan before the shootings. They rejected administration claims the information could compromise the pending prosecution of Hasan.
Lieberman and Collins said the Defense Department and FBI had turned over some documents to their committee but they primarily involved background material.
The Justice and Defense Departments officials sent a joint letter on Monday to Lieberman and Collins telling them that turning over the information and its disclosure could compromise the case against Hasan.
"We regret your dissatisfaction with our positions, but ask that you defer committee actions that would complicate our prosecution efforts or give rise to a perception that our decision-making about them is subject to political pressure or influence," they said.
They added that making FBI and Defense Department agents available for interviews was against long-standing policy.
The subpoena could be an unwanted distraction for a White House already under pressure to cut unemployment, pass climate change legislation and regulate the financial industry.
Lieberman said his committee wanted to "put to rest the still unanswered questions of why Major Hasan was not stopped before turning on his fellow Americans."
Reviews ordered by the Pentagon and White House have exposed shortcomings in both intelligence and oversight. (Source Reuters)