The loss of income from the furloughs could make members of the intelligence community more susceptible to bribes, Clapper said during a Senate Judiciary Committee hearing on Wednesday.
"This is a dreamland for foreign intelligence service to recruit, particularly as our employees already ... [subjected] to furloughs driven by sequestration, are gonna have even greater financial challenges," he said.
"I don't feel that I can make such a guarantee to the American people," Clapper replied.
In a letter sent to Clapper on Friday, the Iowa Republican pushed back hard against that claim.
"Respectfully ... your testimony appears to reflect both a misreading of the law and a failure of leadership" in the face of the ongoing shutdown, Grassley said Friday.
The intelligence chief is legally obliged to keep civilian workers within the intelligence community deemed critical to national security priorities.
Intelligence employees characterized as critical "for the safety of human life and protection of property" under the White House's shutdown guidelines "should have never been furloughed in the first place," according to Grassley.
That said, the Iowa Republican is joining the chorus of defense and national security lawmakers demanding the Obama administration put civilian employees back on the government payroll.
"It is incumbent upon you, as the leader of the [intelligence community], to press the president and Congress to work together to pass emergency legislation to adequately fund the [community] during the shutdown without delay," Grassley said.
His comments echo those of Senate Armed Services Committee ranking Republican Sen. Jim Inhofe (Okla.), who is pressing the Pentagon to reinstate civilian workers at the Defense Department.
President Obama signed the "Pay Our Military Act," which ensures U.S. service members will continue to receive regular paychecks, as well as the civilian employees deemed exempt from the shutdown.
That said, Inhofe wants that authority under the act to be expanded to "the broadest extent possible" to cover those furloughed Pentagon workers.
While all service members will continue working during the shutdown, about half of the department’s 800,000 civilians are being furloughed.
On Thursday, members of the House Rules Committee approved a full House vote on legislation to pay furloughed federal employees at CIA and other intelligence government agencies.
The Preserving Our Intelligence Capabilities Act, which directs the Treasury Department to extend all unobligated funds to finance civilian payrolls within the intelligence community, could be brought to the House floor as soon as next week.
It remains unclear whether the Democratically controlled Senate will follow suit.