Santa Fe County is investigating a high-level employee’s claims the county is using a flawed system designed by “uneducated and unqualified” staff to estimate construction costs on projects that are then being underfunded and cheaply built, shortening their lifespan.

“I will no longer place my engineering stamp on any project that I feel is inadequate due to funding constraints,” Diego Gomez, a projects engineer in the county’s Public Works Department, wrote in an email to County Manager Katherine Miller, county commissioners and others. “The process … is a gross mismanagement of tax payer [sic] dollars.”

Gomez also accused the new public works director, Tony Flores, who was recently moved into the position after serving as deputy county manager for several years, of abusing his authority and creating a hostile work environment.

The investigation comes after a shake-up of top-level staff at the county that included Flores replacing Michael Kelly, who was demoted to deputy director.

“In a directors meeting on Tuesday July 30 Mr. Flores screamed at the top of [his] lungs for over 30 minutes,” Gomez wrote in the email obtained by The New Mexican. “Some of his statements were as follows, ‘I am not [expletive] here because I want to be here. I’m here because you [expletive] don’t know how to do your [expletive] job, and I have until December to clean this place up. If I go down, I’m taking every one of you with me.”

Gomez declined to comment, saying all media inquiries must go through county spokeswoman Carmelina Hart. Flores did not return a message seeking comment.

“We take allegations of mismanagement and waste of taxpayer dollars seriously, and retaliation of any kind against employees who make such allegations in good faith is strictly prohibited,” Greg Shaffer, interim deputy county manager, wrote in a response to Gomez’s email.

“You will be contacted shortly by people tasked with investigating your allegations of mismanagement and waste of taxpayer dollars,” Shaffer added in his email to Gomez. “It is important that you preserve all evidence you have related to your allegations, including, but not limited to, emails, notes, engineering drawings, and audio or video recordings.”

Shaffer wrote a separate email to county commissioners, who were copied in the initial email by Gomez, that the allegations “are being looked into.”

Hart confirmed the county is conducting an investigation but declined to go into specifics.

“Santa Fe County takes allegations of mismanagement and waste of taxpayer dollars seriously,” Hart said Wednesday in an email. “The County Manager’s Office responded to the employee on the day it received his email, and … an independent investigation, conducted by a third-party contractor, has been launched into his allegations concerning projects.”

Regarding Flores, County Commissioner Anna Hamilton, said in an interview Monday, “He was a fabulous deputy manager, but he was also so uniquely qualified to try to … help ongoing issues in Public Works with how to manage projects so they were done efficiently and on time and on budget. He agreed that he was really good at that and agreed to move over, wanted to take that challenge.”

One of Gomez’s chief complaints was about the county’s so-called maximum allowable construction cost system, or MACC, which Hart said is project-specific.

“It establishes the maximum construction cost for a project, to which the project is to be designed,” she wrote.

The problem, Gomez claimed, is that the system was established by staff who didn’t know what they were doing.

“As projects engineer I have been told many times that I have to build and design projects within the MACC,” he wrote. “The projects that have been selected for construction do not have adequate funding to build them properly and most of the projects do not justify improvements. The recent road projects in the Stanley area cost $3.5 million and are already falling apart. There was not enough funding to allow proper design and construction of these roads.”

With the exception of the road projects in the Stanley area, which apparently includes a pavement restoration project on a rural road leading to the home of the county’s deputy public works director, Robert Martinez, Hart noted that Gomez’s allegations were general and didn’t identify specific projects.

“Nor does he identify specific staff who allegedly set the MACC on the unidentified projects,” she wrote. “Given that and that our independent investigation is not complete, we cannot comment on the education and qualifications of county staff, the adequacy of funding for specific projects, or the structural integrity of specific roads.”

However, Hart said the county was aware of multiple road projects in which Gomez requested and received additional funding.

“We do not recall any requests by Mr. Gomez for additional funds for a road project that got to the county manager or Board of County Commissioners level that was denied,” she wrote.

In addition to concerns over the MACC, Gomez raised a red flag over Flores’ alleged behavior, which he called inappropriate and threatening.

“When I commented that if the people in the room [at the July 30 directors meeting] were to be held accountable, the other departments also need to be held accountable for their parts in the project delays,” he wrote in his email. “Mr. Flores responded by yelling, ‘I’m not in charge of other departments. I’m in charge of this [expletive] department and if you keep this attitude up, you will be the first one out of here.”

Gomez questioned whether Flores, who has served as facilities director, purchasing director and capital projects manager during his tenure with the county, should be supervising anyone, much less an entire department, if he “showed his true colors in that meeting.”

“I have retained legal counsel and I know my rights in accordance with the Whistleblower Protection Act,” he wrote. “I will continue to come to work and perform my duties to the best of my ability, however, I will no longer tolerate the unethical behavior.”

Follow Daniel J. Chacón on Twitter @danieljchacon.