Despite concerns from the civilian commission overseeing the Fire Department, the water-delivery system set to receive a major upgrade with a June bond measure will be turned over to the San Francisco Public Utilities Commission.

The transfer will save the Fire Department money, but will put control of the system in the utility agency’s hands. Mayor Gavin Newsom ordered the transfer last week.

The SFPUC was going to start paying the costs of maintaining the water system that supplies most of the fire hydrants around The City, but it ran into resistance from the Fire Commission, which fought to keep control under the Fire ­Department.

Commissioners worried that the pipes and cisterns that carry water intended for battling fires would end up being used for other purposes, such as for drinking water and cleaning out the sewer system.

But with a $412 million bond measure meant to fix the Auxiliary Water Supply System on the June 8 ballot, the debate suddenly ceased.

The agreement will divert money to San Francisco’s general fund and was approved during the budget season earlier this year. The deal will save the Fire Department about $2.4 million a year and the SFPUC will pay the department $500,000 for miscellaneous equipment, according to Newsom’s order.

The SFPUC’s water enterprise is funded through rates that come in from about 2.4 million customers throughout the Bay Area, and the Fire Department is funded through the general fund.

Saving money has a lot of interest in these pressing economic times, said fire Commissioner Victor Makras, who was an outspoken opponent of the transfer. And retrofitting of the system should fall under the SFPUC, he said.

The City would only have the chance to retrofit the system if the bond measure passes with two-thirds of the vote.