In a blistering letter sent to President Obama on Monday, the head of the agency that investigates whistle-blower complaints in the federal government criticized the Department of Veterans Affairs for not digging deeper into widespread allegations made by its own employees of poor or severely delayed patient care for veterans.

In the letter, Carolyn N. Lerner, head of the Office of Special Counsel, asserted that Veterans Affairs officials consistently had used a “harmless error” defense to dismiss as trivial numerous claims of shoddy patient care or long waiting times made by department employees in recent years. Ms. Lerner criticized the department, along with its Office of the Medical Inspector, for a longstanding pattern of refusing to use whistle-blower complaints to fix serious medical problems.

The Office of Special Counsel, an independent agency within the executive branch, is reviewing more than 50 pending complaints from Veterans Affairs workers alleging harm to patient safety or health; 29 have already been forwarded to the department for further investigation. That is more than one-quarter of all the pending cases the Office of Special Counsel has referred for investigation across the entire federal government. The office is also investigating about 60 cases involving Veterans Affairs employees who alleged they faced reprisals for raising concerns about patient care.

Ms. Lerner said she was encouraged by recent statements by the department’s acting secretary, Sloan D. Gibson, in support of whistle-blowers’ playing a critical role at the department. Mr. Gibson took over three weeks ago, after Eric Shinseki, who had led the department since President Obama took office, resigned amid a widening scandal over falsified waiting lists at several veterans hospitals and clinics.