For FBI agents who've devoted their careers to protecting the U.S. homeland or rooting out major crime across the country, this certainly was not the message they wanted to read at 5:49 p.m. on Wednesday, the second day of the government shutdown: "Unfortunately, whether you are in an 'Excepted' or 'Non Excepted' status, there may be a financial impact to your paycheck."

In other words, if you're furloughed or not, your salary this year may be different than you planned.

"Only if congressional action is taken to pass legislation which allows for the retroactive payment of compensation for the time period encompassing the government shutdown, then all employees will be compensated for that time period," said the email to FBI employees, obtained by ABC News.

In many ways, the impact of lawmakers' failure to keep the federal government running seems theoretical. But it's not theoretical to the scores of FBI agents now in terrorist-torn Kenya who aren't being paid as they try to figure out if the group that launched a deadly assault in a Nairobi mall last month could strike the U.S. homeland.

Nor is it theoretical to the FBI agents, CIA operatives, Border Patrol agents, homeland security investigators, airport screeners, firearms agents, U.S. marshals and other intelligence and law enforcement officials who reported for duty across the country this morning without knowing if they'll ever see a paycheck for their current efforts to protect the nation.

"I wonder why all the fat cats in Washington are getting paid to argue about [the federal budget], and why are we getting caught up in it," said one frustrated FBI agent, a 15-year veteran who works counterterrorism cases in an unusually expensive U.S. city. "This is horrific."

At FBI headquarters in Washington, half of the staff - the "non excepted" workers - have been told to stay home, according to one official.

"Life as an FBI agent is pretty tough" even without furloughs, forcing many agents to commute 50 miles or more each day because they can't afford to live any closer to the city they work to protect, the FBI agent told ABC News.

Those in the agency accept the job and do the work knowing they are serving the public. One of the only things they ask for in return is "a steady paycheck," the agent said, speaking to ABC News on the condition of anonymity.

"Now one of those things is being taken away," the agent said, adding that getting compensated sometime later "does not help agents in [an expensive] city who live paycheck to paycheck."

What's more, FBI agents and other federal workers currently on the job who require medical attention during the government shutdown are considered furloughed if they leave for a doctor's appointment. They may never be paid for that time seeking medical help.

"During a government shutdown, by law, there is no paid leave (annual, sick, court, military leave, restored annual leave, comp, or leave for bone marrow or organ donation), no matter when it was approved," the email to FBI agents late Wednesday said. "Unfortunately, there are no exceptions. … In other words, excepted employees can go to a doctor's appointment but will be considered furloughed for the hours they are absent."

The FBI agent who spoke to ABC News had a significant surgery scheduled for next week but felt compelled to cancel the surgery in the wake of the government shutdown.

"Now this is affecting my physical well-being," the agent said.

ABC News has chosen not to describe the surgery to help protect the FBI agent. FBI officials have directed agents not to speak to the media about how the government shutdown is impacting them.

In addition, because of the government shutdown, the agent who spoke to ABC News was also adjusting plans for the long-term future.

"I'm going to be putting less into my retirement so that I get more take-home and can pay my bills," the agent said. "That's really sad."

Still, the FBI brass concluded its message to employees with this: "[T]hank you for your patience and dedication to the FBI during this difficult time."

ABC News' Pierre Thomas contributed reporting.