The Department of Veterans Affairs is in the process of overhauling the country’s oldest electronic health record system at the country’s largest hospital network. Even if it goes smoothly, planners have repeatedly warned, it will be an extremely complicated task that will take 10 years and cost more than $16 billion.

And so far, it is going anything but smoothly.

The new health record software is supposed to increase efficiency and speed up care in the beleaguered veterans’ health system, which serves more than nine million veterans. But when the department put it into use for the first time in October at a V.A. medical center in Washington State, it did the opposite.

The department’s inspector general issued two scathing reports on the rollout this week. One found that the company that was awarded a no-bid contract by the Trump administration to do the overhaul underestimated costs by billions. The other report said the training program for hospital staff that the company created was so flawed and confusing that many employees considered it “an utter waste of time.”

All the employees who went through the training at the first hospital to use the new health record system, the Mann-Grandstaff V.A. Medical Center in Spokane, Wash., were given a test afterward to see whether they had learned to use it proficiently. Nearly two-thirds failed, the report said.

Soon after Mann-Grandstaff began using the software in October, employees started to complain that the training was rushed and inadequate. Tasks that had been simple before became complex. The new system was so cumbersome that productivity decreased by about one-third, the inspector general’s report said.

“Staff were exhausted, struggling, felt that they were failing and morale was low,” the report said.

The software upgrade also came with unexpected extra costs, the inspector general reported, because the department will have to spend at least an additional $2.5 billion for new laptop computers and other equipment that can run the new software.

The Department of Veterans Affairs pioneered electronic health records in the 1980s with a system created in-house that is known as Vista. The open-source software used in Vista allowed employees at hospitals across the country to build on and adapt the system to meet local needs. But because anyone could modify it, Vista became a tangled software shantytown of more than 130 systems and thousands of applications. Though in general they worked seamlessly within the veterans’ hospital network, Vista was unable to readily share patient information with the military or with private hospitals.

The department tried several times over the past 20 years to modernize Vista at its 1,500 hospitals and clinics, and spent nearly $1 billion in the process. But the hydra of homegrown code defied all its efforts.

In 2018, the Trump administration signed a 10-year, $10 billion deal with a private medical-records contractor, the Cerner Corporation, to replace Vista and to train the department’s 367,200 health care workers to use the new system.

Spokane was chosen for the trial run, and there were problems from the start, including two postponements. The office overseeing the installation did not consult with the frontline health care workers who would be using it, according to the inspector general.

Employees were not given access to software they could practice on, the report said. Trainers supplied by Cerner were regularly unable to answer employees’ questions about practical use scenarios, and often demurred by saying, “Let’s put that in the parking lot.”

After being inundated with complaints, Representative Cathy McMorris Rodgers, a Republican who represents Spokane in Congress, sent a letter to the Department of Veterans Affairs in March, describing a system that was so confusing it caused veterans to receive the wrong drugs and nurses to break down in tears.

“I am hearing an increasing number of complaints and pleas for help,” Ms. McMorris Rodgers wrote in the letter. She added: “I have one report of a V.A. doctor ordering a veteran two medications, but he received 15 erroneous medications. I have multiple reports of prescriptions being delayed, which in one case caused a veteran to suffer withdrawal. These impacts are dangerous and unacceptable.”

In surveys of hospital employees, two-thirds of those who completed the training said they still could not use the new system without difficulty, the inspector general’s report said.

The department’s official test results told a different story, indicating that 89 percent of employees passed proficiency tests after training. But investigators found that, in fact, only about 44 percent had passed. Department officials in charge of the rollout had “removed outliers” to make the official results look better, and deleted additional data that may have shown further problems with training, the inspector general’s report said.

The department said on Friday that it took the inspector general’s findings “very seriously,” but it declined to comment further on the reports.

In a statement, Cerner said: “Cerner is fully supporting V.A. and shares their commitment to getting this right. Together, Cerner and V.A. have made progress toward achieving a lifetime of seamless care for our nation’s veterans and we look forward to continuing this important mission.”

In the spring, as problems were becoming apparent, Secretary of Veterans Affairs Denis R. McDonough, who took over the department this year, suspended the rollout of the new system for three months to review issues. That review is now complete, and the department is expected to announce next week how it will proceed. A veterans’ hospital in Columbus, Ohio, was next in line to get the new system, but Mr. McDonough hinted at a news conference in June that the Columbus installation may be postponed.

The secretary is scheduled to testify before the House Committee on Veterans’ Affairs next week, and is expected to face pointed questioning.

“It is clear from these reports,” Representative Mark Takano, the California Democrat who chairs the committee, said in a statement, that the cost “was vastly underestimated by the previous administration and that there are significant failures with the current staff training program.”

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