The city agency primarily responsible for school modernizations defended its work at a hearing Wednesday before the D.C. Council, responding to an audit that found the District failed to adequately monitor the renovations and violated laws designed to improve transparency, accountability and savings.

Jeff Bonvechio, deputy director for capital construction at the Department of General Services, said that consistent cost overruns have been largely attributable to factors outside the agency’s control, such as the accelerated timelines for school construction, the historic designations of many school buildings and the increasing scope of what was originally supposed to be phased-in modernization projects.

He said he could not comment on some of the audit’s specific findings, which covered fiscal years 2010 through 2013, because he has worked at the agency for less than three months.

He also defended the private contractor the city has hired to manage the school projects day to day after D.C. Auditor Kathy Patterson testified that an estimated 84 percent of a sampling of expenditures the firms submitted had missing or insufficient documentation.

“They are providing quality work and oversight on these projects,” Bonvechio said, pointing to the 75 renovations that have been completed as evidence of their effectiveness.

D.C. Council Chairman Phil Mendelson (D) challenged him on that: “Based on how pretty a building looks, they are doing good work?” he asked. “You can’t say ‘on budget and on time.’ ”

The audit report, released last week, says that the Department of General Services and D.C. Public Schools have not provided basic financial management, allowing the cost of programs to skyrocket.

Council members called oversight of the program “scandalous,” a “runaway train” and “a failure of leadership.”

“Overall, we can do better,” said Nathaniel Beers, the newly selected chief operating officer for the public school system, who mapped out a revised vision for how projects should be managed in the future. The public schools will play a more assertive role in making decisions and providing clear specifications for building requirements, according to his plan.

The school modernization program started in 2006, an effort to improve facilities that had been neglected for decades. In 2007, the city shifted day-to-day management of the program to private contractors McKissack & McKissack and Brailsford & Dunlavey, which formed a joint partnership known as D.C. PEP.

The firm received $37 million in management fees between fiscal years 2010 and 2013, but the city provided only “limited supervision” of the work, the report says. This year, the $9.4 million annual contract funds 30 staff workers.

Council members focused their questions on whether they were getting value for that investment or whether it made more sense to manage projects in-house or hire new contractors.

Officials from D.C. PEP did not testify at the hearing. Deryl Mc­Kissack, principal managing partner of the joint venture, said in an e-mail to The Washington Post that the firms have received national accolades for their work with D.C. Public Schools.

“We believe this audit contains erroneous information, and we stand behind our work on this program,” she said.

The issue of school modernization became pressing this year after dozens of school projects were pushed back in Mayor Muriel E. Bowser’s proposed $1.3 billion, six-year school construction plan. The changes were the result of major cost overruns and a slowdown in capital spending.

The plan stirred frustration in many communities.

“We are at a horrible impasse,” said D.C. Council member David Grosso (I-At Large), chairman of the Education Committee. “There is less and less money to invest in schools and a lot of schools that have not been touched.”

More than six hours into the hearing, Bowser (D) made a surprise visit to testify. She said her administration is committed to having a more honest budgeting process for schools and that she is exploring different options for financing renovations.

“I won’t be the mayor who said we should slow down school construction,” she said. “The growth we are experiencing in the District of Columbia is closely linked to our no-holds-barred investment in our schools.”