The head of the environmental justice program at the Environmental Protection Agency has stepped down, departing the government with a lengthy letter to Scott Pruitt, the EPA's new administrator, urging him not to kill the agency's programs.

Mustafa Ali, a senior adviser and assistant associate administrator at the agency, worked to alleviate the impact of air, water and industrial pollution on poverty-stricken towns and neighborhoods during nearly a quarter century with the EPA. He helped found the environmental justice office, then the environmental equity office, in 1992, during the presidency of President George H.W. Bush.

Ali leaves the EPA as Pruitt, who took office Feb. 17, prepares to implement deep cuts in the agency's budget and staff. A Trump administration proposal would cut the EPA's $8 billion budget by $2 billion and reduce its roster of 15,000 employees by 20 percent. An internal memo obtained by multiple news outlets on March 1 called for a complete dismantling of the office of environmental justice and elimination of a number of grant programs that address low-income and minority communities. A story in the Oregonian reported that funding for the office would decrease 78 percent, from $6.7 million to $1.5 million.

Justice issues have become an environmental focal point in recent years—most recently in the battle to clean up lead-contaminated water in Flint, Mich., a largely African-American community, and in the fight to stop the nearly completed Dakota Access pipeline just upstream of the Standing Rock Reservation in North Dakota.

"I think it's going to be one of the major civil rights issues of the 21st century," said Benjamin Wilson, head of the National Environmental Justice Conference and chairman of the law firm Beveridge & Diamond. "It's going to become increasingly not simply local but regional, national and international in scope."

Ali said he has received no indication that the adviser position or his job as assistant associate administrator in the agency's Office of Enforcement and Compliance Assurance will be filled by the Trump administration. EPA officials declined to comment on the positions.

The EPA made strides during the Obama administration to address environmental justice concerns, including incorporating equity into regulatory decision-making, and adopting a long-term strategy in its EJ 2020 Action Agenda. The agency was, however, heavily criticized for not doing enough to address environmental concerns of low-income and minority populations.

Ali said in an interview that he considers the shielding of poor and minority neighborhoods from the effects of pollution a crucial function of the EPA, but that the agency's new leaders have not given "any indication that they are focused or interested in helping those vulnerable communities. My values and priorities seem to be different than our current leadership and because of that I feel that it's best if I take my talents elsewhere."

EPA Administrator Scott Pruitt. Credit: Aaron P. Bernstein/Getty Images

Still, in his resignation letter, which was devoid of rancor, Ali urged former Oklahoma Attorney General Pruitt, a longtime opponent of EPA regulation, to reconsider proposed cuts to environmental justice programs. "When I hear we are considering making cuts to grant programs like the EJ small grants or Collaborative Problem Solving programs, which have assisted over 1,400 communities, I wonder if our new leadership has had the opportunity to converse with those who need our help the most," Ali wrote. "I strongly encourage you and your team to continue promoting agency efforts to validate these communities' concerns, and value their lives."

Meanwhile, the power that Ali once wielded inside the EPA has been dissipated. His position as senior adviser to the EPA administrator was eliminated in January when Obama's EPA chief Gina McCarthy left, he said.

"I am heartbroken that Mustafa feels that his time of productivity in the agency has passed," McCarthy said in an interview. "He managed the interagency working group on environmental justice," she said, referring to a conclave of federal agencies that met to discuss common concerns. "So when I say we brought actions and strategies to the table, it wasn't just EPA, it was throughout the federal government."

Part of the environmental justice program's strategy was to help leverage its relatively small grants into large programs. The town of Spartanburg, South Carolina, for example, received a $20,000 environmental justice grant to help clean up contaminated industrial sites in the town. Spartanburg ultimately raised more than $270 million from public and private sources and used the recovered land to build housing, a job training facility and health centers.

"You're talking about a community that was devastated and that raised itself up because you had great community members and they had somebody who listened to them at the federal government," McCarthy said. "Mustafa was one of those people. I went to that community. I sat with the mayor. He gave me a key to the city. We were sitting in a community center that had been developed as a result of this small start, where somebody paid attention to that community and it happened to be EPA."

Cynthia Giles, assistant administrator for the Office of Enforcement and Compliance Assurance in the Obama administration, cites the town of Tonawanda, New York, to which the EPA gave a small grant to conduct ambient air monitoring. The grant "ultimately led to a criminal case that EPA brought against Tonawanda Coke Corporation for high levels of benzene emissions," Giles said.

Giles said there is no economic justification for killing the justice program. "The money that is involved is not noticeable in the overall scheme of budgets," she said. "The only reason to eliminate it would be to send a message—that they don't care about the needs of the most vulnerable communities."

"We've had both [Republican and Democratic administrations] over time and none of them tried to do anything to destroy what the previous administration had done," Ali said. "Folks are just hoping that this one will wake up and see value in continuing this important work."

Yet Ali sees nothing in Pruitt's background to support that hope. He repeatedly sued the EPA for its efforts to regulate CO2 emissions, mercury and other forms of pollution. "When the administrator was in Oklahoma I do not know of any time that he made environmental justice a priority," Ali said.

Pruitt tweeted last month he was dedicated to working with "stakeholders—industry, farmers, ranchers, business owners—on traditional values of environmental stewardship."

I'm dedicated to working w/stakeholders - industry, farmers, ranchers, business owners – on traditional values of environmental stewardship. — Administrator Pruitt (@EPAScottPruitt) February 17, 2017

Some of the responses the tweet garnered included: "What about environmental advocates?" "What about...people w/o access to safe water & air? Our children?" And "what about ordinary citizens."

In a February statement, advocacy group We Act for Environmental Justice said of Pruitt: "His record indicates he lacks awareness or concern for communities impacted by asthma and other environmental health-related issues."

Ali, who grew up near a coal-fired power plant in West Virginia, interned in the office of William Reilly, the agency's third administrator, before joining as a staff member in the newly formed office of environmental equity in Nov. 1992. From 2007-2008, Ali worked on Capitol Hill in the office of Congressman John Conyers before returning to the EPA. He proudly boasts that he has worked on environmental justice issues in more than 500 communities.

"His work and the work of the EPA has helped empower people, and whenever we can have a clear articulation of the issues, it's amazing the common ground that can be reached by people on opposing sides," Wilson said. "But if we never have that discussion, that frustration festers and that is never good."

Ali will join Hip Hop Caucus as a senior vice president. The group is a non-profit that aims to promote political activism for young U.S. voters through hip-hop music and culture. He is scheduled to speak Thursday at an environmental justice conference in Flint, in his first public appearance with the organization.

"What I'm hoping to do is highlight that environmental justice needs to continue to happen," Ali said, "that there are opportunities to make it happen, and that if we don't do it there will be huge public health impacts."