From counterterrorism investigations to cybersecurity protections, critical elements of the country's national security infrastructure are showing signs of strain.
"From a security standpoint we are letting our guard down. If this shutdown ended tomorrow, I fear that the damage already done to our security will be months if not years," former Homeland Security Secretary Jeh Johnson, who served under President Barack Obama, said Thursday at an event with former senior DHS officials.
On Wednesday, Johnson, along with former Trump White House chief of staff and DHS Secretary John Kelly and three other former secretaries of homeland security, sent Trump and members of Congress a letter calling for full department funding and an end to the shutdown.
"As former secretaries of the Department of Homeland Security (DHS), we write to you today with a simple message -- fund the critical mission of DHS," wrote the bipartisan group of Kelly, President George W. Bush alums Tom Ridge and Michael Chertoff, and President Barack Obama alums Johnson and Janet Napolitano.
The Pentagon and intelligence agencies are fully funded, and federal law and Office of Management and Budget guidelines direct even unfunded agencies to maintain operations that involve "the safety of human life or the protection of property." But at key agencies like the Departments of Justice and Homeland Security, an unpaid work force and tightened operational budgets are having an impact.
Here's a rundown of impact the shutdown is having:
Counterterrorism investigations
The FBI has lost several informants that had penetrated groups at the center of terrorism investigations, a joint terrorism task force coordinator said in a report released by the FBI Agents Association, an advocacy organization for FBI agents.
The account is one of a number from anonymous agents who took the extraordinary step to highlight how the lack of funding has kneecapped their operations in a report released Tuesday.
"The failure to fund the FBI is making it more difficult for us to do our jobs: to protect the people of our country from criminals and terrorists," said Tom O'Connor, the president of the agents association, which represents most of the bureau's active duty special agents.
Late Tuesday the FBI distanced itself from the report.
"This report is a product of the FBIAA, a nonprofit professional association, and was not issued by the FBI," the FBI said in a statement.
Cybersecurity protections
Central components of the nation's cybersecurity infrastructure have ground to a halt as the Department of Homeland Security has gone unfunded.
At the Cybersecurity and Infrastructure Security Agency, an arm of DHS, the scaling back of personnel has forced the agency to end "a variety of critical cybersecurity and infrastructure protection capabilities," the agency said in a statement.
While the agency has "maintained baseline operational capabilities supporting national security," experts say the lack of offensive action being taken leaves the country's cyberspace vulnerable.
"Every day that we are not at full strength, fully engaged in understanding what our adversaries are doing, developing policies to innovate to match their adaptability and innovation is a day we fall behind," said Suzanne Spaulding, former undersecretary for the National Protection and Programs Directorate at DHS, the predecessor of CISA.
DHS spokesman Tyler Houlton told CNN that the department is "is fully capable of carrying out our mission of securing the country during a lapse in government funding."
"Nearly 90 percent of DHS employees are currently working on essential national security projects and programs without a paycheck. There is no question that unpaid DHS employees and their families are facing financial constraints and sacrificing greatly, which is why we call on Congress again to fully fund the Department and provide us the resources we need to keep America safe," Houlton added in a statement.
Diplomatic impact
Last week the State Department ordered all employees back to work beginning on Sunday, after finding enough money to pay them for one pay period.
Prior to the recall approximately 23% of US direct hire overseas employees and 40% of direct hire domestic employees had been furloughed.
But the shutdown has had an adverse effect on the ability of the diplomats to engage with the foreign partners and adversaries.
"As if the current administration had not hurt our image as a reliable partner enough, I now have people asking why I cannot meet with them," a foreign service officer told CNN.
A host of high-ranking US officials scheduled to attend the World Economic Forum skipped their flights to Davos, Switzerland, this month after Trump canceled the delegation, citing the ongoing shutdown. As a result, the US did not participate in a sideline meeting on the Syrian civil war and a tête-à-tête with the Chinese.
And last week, the State Department canceled an international conference on export control and border security set to be attended by 85 countries, citing "uncertainty associated with the continuing partial U.S. federal government shutdown."
Secretary of State Mike Pompeo told CNN that he hoped "the shutdown will end quickly" and that he is sure American diplomats are "capable of rising to the challenge."
"Being an American diplomat is a high and unique calling. 325 million Americans are counting on our diplomats to advance their interests, and to be an unprecedented force for good among nations. These are hard jobs that live up to their billing as public service. I hope that our motivation in the tough times -- and I hope the shutdown will end quickly -- will be the well-being of our fellow Americans. I'm asking a lot of our colleagues. But I know we have the finest diplomatic corps in the world that is capable of rising to the challenge," Pompeo said in a statement.
Coast Guard operations
On January 15, thousands of active-duty Coast Guard service members, who serve under the Department of Homeland Security, did not receive their paychecks, marking the first time in history that US service members were not paid during a lapse in government funding.
That's fueling anxiety and cutting into operations, active duty officials said.
At one Coast Guard air station, about 10% of routine, non-life-saving flights have been canceled by pilots who said they are too distracted and stressed to fly safely during the shutdown, according to a pilot who spoke to CNN on the condition of anonymity.
"We're five plus weeks into the anxiety and stress of this government lapse and your non-pay," Commandant Adm. Karl L. Schultz said in a video tweeted out as a message to service members on Tuesday. "You as members of the armed forces should not be expected to shoulder this burden."
Airport safety
Transportation Security Administration officers, who are required to work without paychecks through the partial government shutdown, have called out sick from work some days of the shutdown at more than double the rate of last year, according to the agency.
On Tuesday, the absentee rate was 7.4%, up from 3.2% a year earlier, TSA said. Wait times for flyers on Tuesday remained within TSA averages at most airports, though a number of hubs have seen delays in security lines.
The big question is "How are they filling the void?" one of veteran TSA official said, voicing concern about the impact on security. "If you're not seeing long wait times at airports, there's something on the security side they're not doing."
In a statement Wednesday, the TSA said security is not being compromised by the call outs.
"In coordination with airport and airlines partners, TSA continues to carry out its mission by optimizing resources, managing consolidation efforts, and ensuring screening lanes are properly staffed. Security will never be compromised.
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