The tribe is facing a $23 million cut to its budget since Congress failed to halt sequestration, an across-the-board budget cut that went into effect March 1.
The cuts were required by the 2011 Budget Control Act and will equate to about $42 billion less in federal spending this year.
"The end of the month is when we'll really see it," said Navajo Nation President Ben Shelly on Wednesday during a visit to Shiprock.
The Navajo Nation receives more than $330 million of its estimated $500 million budget from federal funding, Shelly said.
"A lot of employees are worried," Shelly said.
Among the departments with the most to lose are the Department of Public Safety, Department of Din Education, and Indian Health Services, according to tribal officials.
Navajo Nation officials in Washington, D.C., currently are advocating for leniency for the tribe, and others, because Indian Country has more to lose, officials said. Officials also are arguing that the federal government has an obligation to Native Americans because of treaties signed in the 1800s, vowing that the federal government would provide care to the tribes.
"They have a contract with us," Shelly said.
The cuts have been made, however, and there is little likelihood that anything can be done at this point, some say.
Also the tribe has about $23 million in its reserved fund, which could be used for anything and pulled at anytime, said LoRenzo Bates, chairman of the Navajo Nation Council Budget and Finance Committee.
It is not known whether the tribe will pull any of those funds, but it is likely many members will be tempted.
The Navajo Nation, like many other tribes, struggles with high rates of poverty, along with high rates of crime and substance abuse.
While the cuts likely will directly affect departments from the top down, the indirect effects will hurt everyone, officials said.
"The poor people, it's going to affect them the most," Shelly said.
Many employees in federally funded agencies are concerned about furloughs, but the general public appears more concerned about longer wait times for services.
Services on the reservation already come relatively slowly when it comes to hospital visits, police calls, and business applications.
Even the departments that do not rely on federal funding, such as the Office of the Public Defender, are worried about how the cuts might affect their services.
"It's a problem that could come back to hit us," said Kathy Bowman, director of the Navajo Nation Office of the Public Defender in Window Rock.
Offices such as hers could be impacted later if the tribe ultimately decides to cut down its general fund, which is funded by the tribe, to help pay for programs that would have been receiving federal dollars.
"It would seriously affect us because we're already seriously underfunded," Bowman said.
Many employees in Window Rock, however, say they have been informed that changes are in the works.
Officials, however, say that nothing will be set in stone until the end of the month, when the process for implementing the cuts is expected to be clearer.
"I don't know what they're thinking," Shelly said, noting that he does not agree with sequestration, especially not its impact on the tribe.
Jenny Kane may be reached at email@example.com; 505-564-4636. Follow her on Twitter @Jenny_Kane