A $3.2 million investment of public money to build a fluoridation system for San Diego’s water supply could end up going down the drain.

That grant from the First 5 Commission of San Diego, which spends tobacco-tax revenue on early childhood programs, will set up the program. Another $700,000 from the commission will operate and maintain the system for two years.

Beyond that, there is no money from the city or any other agency to sustain the program, touted as a way to battle tooth decay in children. That would mean the pipes and tanks would sit empty and unused.

“It would be a tragedy if San Diego gave up on this public health benefit after two years,” said Dave Schubert, a professor at the Salk Institute for Biological Studies in La Jolla and a longtime proponent of fluoride. “It’s not something you can start and stop. It requires a continuous exposure.”

Contractor J.R. Filanc Construction Co. recently began installation of the fluoride equipment at San Diego’s three water treatment plants. It includes tanks to store liquid fluoride, pipes and pumps to inject it into the water supply and instruments to monitor the system.

San Diego plans to start adding fluoride to tap water by the end of November.

First 5 officials say they gave San Diego a two-year window to create financing for a sustained fluoride program even though the state only required one year of funding.

“It has always been the Commission’s intent that its initial investment in fluoridation will be followed by long-term funding, directly from cities or water districts receiving First 5 funds for fluoridation,” said Barbara Jiménez, executive director of the organization.

But Jim Fisher, assistant director of the city’s Public Utilities Department, said, “I don’t think we have done anything” toward that goal since accepting the First 5 grant.

Alex Roth, a spokesman for Mayor Jerry Sanders said it’s “premature to make any decision” about if, or how, fluoride will be paid for in the future.

The future of fluoride in the city has been uncertain from the start.

A city staff report on the project in June 2008 said, “The city need not operate the fluoridation system once it is installed unless outside funds are thereafter provided in any fiscal year to cover the noncapital and maintenance costs.”

Smaller water agencies that wanted First 5’s money for fluoride didn’t get it even though they did commit to paying the ongoing bills.

At the Olivenhain Municipal Water District in Encinitas, general manager Kim Thorner said her board approved an application for a fluoride grant a few years ago in hopes of getting startup funds from First 5.

“They gave the city of San Diego all the money,” said Thorner. “I was sort of disappointed.”

Olivenhain leaders had planned to incorporate the ongoing costs of fluoride into their budget, but never got the startup money to get going.

“Once we switched the fluoride injection system on, we would have run it consistently,” Thorner said.

San Diego accepted First 5’s financial assistance in June 2008 after experts such as Schubert advocated for what he called “the largest and most cost-effective health benefit readily available to the city.”

His views are hotly contested by anti-fluoride activists who link fluoride to cancer and other health maladies and challenge whether the product works as advertised.

Debates about fluoride in San Diego go back at least to 1954, when San Diego residents voted in a special election to ban treatment of city water with “any fluoride compound.”

That language remains, but the City Attorney’s Office said it is “void and has no effect” because it has been superseded by a 1995 state law that requires water providers with more than 10,000 connections to fluoridate water supplies. The state law exempted public water systems from the mandate until “outside funding” was found.

Ray Palmucci, a deputy city attorney, said the state’s pre-emption of the anti-fluoride language in the municipal code means that the city is not barred from using its own money nor is it obligated to continue once external funding dries up.

San Diego was the First 5 commission’s top priority for funding in the region because its leaders said fluoridation of city water would benefit the greatest number of children. In November 2007, when the commission decided to spend money on fluoridation in the county, just over 112,210 children ages 0 through 5 lived in the city — more than 41 percent of the countywide total.