The founding chairman of the board that advises the Massachusetts Life Sciences Center resigned Thursday, questioning the Baker administration’s commitment to the agency.

In a letter sent to the center’s board, scientific advisory panel chairman Harvey Lodish cited the administration’s failure to replenish a capital projects fund that helps finance infrastructure for municipalities and universities seeking to strengthen research and training capabilities in the biomedical field.

“Unfortunately, support from the Baker administration for the [life sciences center] and for the capital projects fund in particular is dwindling,’’ wrote Lodish, a founding member of the Whitehead Institute for Biomedical Research in Cambridge and professor of biology and biological engineering at the Massachusetts Institute of Technology.

Baker’s budget for the coming fiscal year, unveiled last week, did not include money for the center’s capital fund. Administration officials say the capital fund will be part of a separate midyear budgeting process.

Because of the lack of funding, Lodish’s letter said, the advisory board — which evaluates grant and loan requests — is hamstrung. The letter said the center “now lacks the capability to help the many cities and not-for-profit institutions in the Commonwealth develop the next generation of innovative discoveries.’’

“Ultimately,’’ Lodish wrote, “I feel I can no longer lead a scientific advisory board with such diminished advisory capacity and so must reluctantly submit my resignation.’’

Travis McCready, who was named chief executive of the life sciences center last fall, said he and Lodish spoke and he is aware of the concerns.

“I get Harvey’s frustration that the timetable doesn’t work for him, but there’s some budget realities that we have to work out,’’ McCready said.

McCready called the advisory board “an absolutely critical part of what we do and what we’ve been able to accomplish at the center.’’ He said the agency’s capital budget has been tied up in a broader review of capital spending under the Baker administration but a draft is likely to be released in late winter or early spring.

Governor Charlie Baker’s proposed budget for the fiscal year starting July 1 allocates $10 million to operate the Waltham-based life sciences center and $20 million in tax incentives for life sciences companies that create jobs in Massachusetts. It also continues a so-called accelerator loan program for early-stage companies.

But the spending plan did not include the center’s capital fund, which in past years has bankrolled projects ranging from eight life sciences incubators across the state, to a drug development center at Dana-Farber Cancer Institute, to the Sherman Center building at the University of Massachusetts Medical School in Worcester. The center’s capital fund totaled $65 million in the current fiscal year.

In an interview, Lodish said he became frustrated in the last year with the Baker administration’s lack of communication over the future of the capital fund and its commitment to the scientific advisory board. While he has never met Baker personally, Lodish said neither Jay Ash, the housing and economic development secretary who oversees the life sciences center, nor McCready, has given him guidance about the future.

Lodish also said he sensed a reduced commitment to the center in decisions by two Baker cabinet secretaries — Ash and Kristen Lepore, the state secretary for administration and finance — to designate lieutenants to serve on the life sciences center board in contrast to their predecessors who sat on the board themselves. And he objected to the state’s decision to commit $5 million from the agency’s budget to fund a new General Electric Co. innovation center.

“That strikes me as improper,’’ Lodish said. “That’s not part of the [center’s] vision for life sciences. Recruiting a major company is not part of what the capital funds were intended for.’’

McCready said the center was “getting great service’’ from the cabinet secretaries’ designates, Lepore’s chief of staff Dominick Ianno and Ash’s assistant secretary Michael Kennealy. He said the administration agreed to consider funding GE’s planned innovation center, but that work at the center would include life sciences as well as digital health and other fields.

The life sciences center was launched in 2008 to implement an initiative by former Governor Deval Patrick to promote the biotechnology and medical device industries. While state officials have pointed to dozens of companies that have set up shop here and thousands of jobs created because of the center’s capital grants, loans, and tax incentives, some critics have argued that many of the companies and jobs would have come to the state anyway.

Baker administration officials initially weighed the possibility of merging the life sciences center into a larger economic development agency. But the idea was abandoned after strong objections emerged from the life sciences industry.

Bob Coughlin, president of the Massachusetts Biotechnology Council, a trade group, said administration officials have been “all ears’’ in listening to industry leaders while formulating their life sciences strategy.

“They understand the important role the industry plays in Massachusetts,’’ he said.

Coughlin also said Lodish is “a world-renowned scientist and one of the most respected people’’ in the field.

“If the scientific advisory board isn’t doing deals now, maybe it’s not the best use of his time,’’ Coughlin said.

Lodish has been involved with the life sciences center since its inception. He said he suggested the idea of a scientific advisory board to Patrick after the former governor proposed his life sciences initiative, arguing that an independent review of funding proposals would prevent the planned life sciences center from “getting balled up in politics.’’ Patrick eventually asked Lodish to chair the advisory board, which now has 23 members.

But the advisory board chairman, who does not get paid for his work, said he has had little contact from Baker administration officials even after reaching out to Ash and McCready.

“It’s been 13 months since they took over, and I keep getting the runaround,’’ Lodish said. “I don’t know if they understand or value the scientific advisory board. And I lost my patience, so that’s why I’m resigning.’’

Robert Weisman can be reached at robert.weisman@globe.com. Follow him on Twitter @GlobeRobW.