As the federal public defender office in Boston prepares to defend Dzhokhar Tsarnaev, the 19-year-old charged in the Boston Marathon bombings, the lawyers involved face an added challenge: managing the case in the midst of furloughs.

Federally mandated budget cuts known as sequestration could force Tsarnaev’s lawyers to take up to 15 days of unpaid leave before the end of the fiscal year on September 30. Lawyers familiar with the office said it is feeling the pinch in other ways, including leaving vacant positions unfilled.

The Executive Committee of the Judicial Conference approved a sequestration plan last week that included up to 15 furlough days for federal public defender offices nationwide. The plan slightly lowered the maximum furlough days facing the Boston office, which was planning for up to 16.5 days, according to the U.S. District Court for the District of Massachusetts.

Representatives of the defender office and the court could not be reached to confirm the number of furlough days that lawyers and non-attorney staff in Boston must take.

"There’s no doubt that the sequester is going to affect the administration of justice in general, in Boston, and with this case specifically," said John Cunha Jr. of Boston’s Cunha & Holcomb, former president of the Massachusetts Association of Criminal Defense Lawyers.

Thirteen attorneys serve in the Boston federal public defender office. The furloughs would coincide with the early weeks of Tsarnaev’s defense, which Cunha said is a "crucial" time. "You start to figure out where you are and where the government is and where they’re going to go and how to protect this person’s rights." He added that the defender office hasn’t filled vacant positions under sequestration.

Prosecutors face furloughs under sequestration as well. Still, Tamar Birckhead, a former assistant federal public defender in Boston and professor at University of North Carolina School of Law, described the situation as "David and Goliath" because the U.S. attorney’s office in Boston was backed by the U.S. Department of Justice.

"People will pitch in and do what they can, but it is an unfortunate circumstance," Birckhead said. "It could result in a delay of a possible resolution of the case, which I’m sure is not what the public wants to see."

On Monday, a federal magistrate judge unsealed a criminal complaint accusing Tsarnaev and his brother, Tamerlan Tsarnaev, 26, of planting bombs near the finish line of the Boston Marathon that killed three people and wounded scores more. Dzhokhar Tsarnaev was charged with one count of using and conspiring to use a weapon of mass destruction resulting in death and one count of malicious destruction of property by means of an explosive device resulting in death; his brother died on April 19 in a shoot-out with police.

Tsarnaev is represented by federal public defender Miriam Conrad and two other lawyers from the Boston office, William Fick and Timothy Watkins.

Tsarnaev’s defense team has already asked for assistance. As local prosecutors and the U.S. Department of Justice weigh whether to seek the death penalty, Conrad asked on Mondaythat the court appoint two additional lawyers qualified to handle capital cases. The defender office, working with the Federal Death Penalty Resource Counsel Project, will recommend lawyers to the court for appointment.

Federal law requires that at least one lawyer appointed for a defendant facing the death penalty have capital case experience. Tsarnaev’s lawyers will have two opportunities to weigh in, once before the local prosecutor and once before the Justice Department; the final decision rests with Attorney General Eric Holder Jr.

David Hoose of Sasson Turnbull Ryan & Hoose in Northampton, Mass., said he expected out-of-state lawyers would be appointed, given the lack of lawyers in Massachusetts qualified to handle death penalty cases; Massachusetts lacks a state death penalty. Hoose is qualified, but said he couldn’t join Tsarnaev’s defense team even if asked because he’s handling a capital case in Rhode Island.

"This is a huge amount of work," he said. "Whoever takes this on is going to have to severely limit whatever else they do for the next couple of years."

Conrad has worked for the federal public defender office in Boston since 1992 and took the top job in 2005, which also includes overseeing federal public defender offices in New Hampshire and Rhode Island. She’s had experience defending high-profile suspects, including Richard Reid, the so-called "shoe bomber" who was sentenced to life in prison after attempting to detonate explosives in his shoes on an airplane in late 2001.

Handling big cases in the national spotlight such as Reid’s or Tsarnaev’s is a rare experience for a public defender, Hoose said. "If you’ve had one, you’re probably in a class by yourself," he said.

Mark Pearlstein, a partner at McDermott Will & Emery and former federal prosecutor in Boston, said Conrad was "a genuinely outstanding lawyer" and her office was held in high esteem across the bar.

"She’s got enormous credibility with the judges and other personnel in that courthouse and with the U.S. attorney’s office," said Pearlstein, who also serves as a court-appointed lawyer for indigent criminal defendants in the Massachusetts federal court. "She’s very, very highly regarded as being a formidable advocate and a very straight shooter."

Tsarnaev agreed to voluntary detention during his initial appearance before a judge on Monday at a Boston hospital where he was recovering from injuries sustained before his arrest. A probable cause hearing is scheduled for May 30.

Contact Zoe Tillman at ztillman@alm.com.