The U.S. Patent and Trademark Office has almost no way to know if patent examiners are doing their jobs well, the agency’s watchdog concludes in a report that raises concerns about the quality of thousands of patents issued each year.

The sharply critical report issued Monday by the inspector general for the Commerce Department, the patent office’s parent agency, found overall deficiencies with quality assurance that put at risk the federal government’s role in protecting new ideas through the issuance of patents and trademarks.

The weaknesses “make it difficult to distinguish between patent examiners who are issuing high-quality patents and those who are not,” the 30-page audit by Inspector General Todd J. Zinser concludes.

The criticism comes eight months after the Alexandria-based office’s award-winning telework program came under fire. An internal inquiry prompted by whistleblower complaints to the inspector general found that some of the 8,300 patent examiners, about half of whom work full-time from home, repeatedly lied about the hours they were putting in, and many were receiving bonuses for work they didn’t do.

When supervisors had evidence of fraud and asked to have the employees’ computer records pulled, they were rebuffed by top agency officials, ensuring that few cheaters were disciplined, investigators found.

But when top agency officials turned over the findings to Zinser’s office, the most damaging revelations had disappeared. The decision by senior leaders to filter out the abuses led to congressional hearings and a pledge to monitor telework more closely.

Monday’s revelations about weak systems for determining if an examiner is prone to errors echoed some of the issues that came to light last year. They include a management policy that prizes production over quality and appears to leave supervisors without a strong hand to monitor their employees’ work product.

Investigators found, for example, that the system for evaluating a patent examiner’s performance was “ineffective” at measuring whether they are issuing high-quality patents. From fiscal 2011 through fiscal 2013, they found, more than 95 percent of all examiners received outstanding or commendable ratings for the “quality” element in their annual performance evaluations.

And from fiscal 2009 to 2013, 99 percent of examiners received “quality” ratings that made them eligible for almost $145 million in bonuses, $6,000 in awards per examiner per year.

The investigation was prompted by complaints from companies and inventors applying for patents. Error-free reviews are key to the examination process, in particular to stave off frivolous patent litigation, the report said.

“High-quality patents are generally considered to be those whose claims clearly define and provide clear notice of their boundaries, while low-quality patents are those that contain unclear property rights, overly broad claims, or both,” is how the inspector general defined the importance of accuracy.

While supervisors are required to conduct an in-depth review of a minimum of four patent examinations every year, patent officials had “no records to confirm if these in-depth reviews actually occurred,” investigators found.

When errors are discovered, most supervisors choose to coach the examiner rather than initiate a time-consuming, paperwork-heavy process of documenting the error. Few examiners receive warnings for low-quality decisions, investigators found. And managers are not collecting data on errors that could ultimately improve the quality of patent reviews.

The patent office has an official quality-assurance team that review errors. But the inspector general found fault with the process, which does not require these independent reviewers to record errors when they find them. This is a weakness that “may have underrepresented the true error rate,” the inspector general found.

Two common work practices that have been identified in the past also have the potential to lead to errors, investigators found. These are known in the patent world as end loading and mortgaging. End loading refers to the practice where examiners wait until the end of each quarter to submit their written decisions. Mortgaging allows examiners to receive credit for their work before a supervisor reviews it.

Both practices are vulnerable to errors, the inspector general found, but patent officials have not done enough to stop them. This “may not discourage abuse,” the report says.

The inspector general, not surprisingly, urged the Patent and Trademark Office to improve its quality-control systems with tighter reviews and controls and a performance evaluation system that properly documents errors and allows supervisors to take action against an employee.

In response, USPTO Director Michelle K. Lee concurred with most of the recommendations and noted that the agency has begun to make progress to address errors, including hiring a new, full-time senior executive: Deputy Commissioner for Patent Quality.